Skip to content
Snippets Groups Projects
Commit dbda4ecc authored by cstritt's avatar cstritt
Browse files

initial commit

parents
No related branches found
No related tags found
No related merge requests found
Hide whitespace changes
Inline Side-by-side
Showing
with 959 additions and 0 deletions
.gitignore 0 → 100644
+ 2
− 0
View file @ dbda4ecc
pangenome
\ No newline at end of file
README.md 0 → 100644
+ 20
− 0
View file @ dbda4ecc
# Genome assembly and variant calling from PacBio HiFi reads
This folder contains two Snakemake workflows:
- *assembly*: from PacBio HiFi consensus reads to annotated genome assemblies
- *variantcalling*: combine assemblies into a pangenome graph and call variants from the graph
This is ongoing work, some things will change.
## Requirements
Running the workflows requires [Snakemake](https://snakemake.readthedocs.io) and [Singularity](https://docs.sylabs.io/guides/latest/user-guide/). Both are installed on sciCORE and can be loaded as modules:
```
ml snakemake/6.6.1-foss-2021a
ml Singularity/2.6.1
```
Enter subdirectories for further information.
#<img src="fig.png" width="50%" height="50%">
*Section of a genome graph constructed from diverse MTBC genomes. It shows a nested structural variant: an IS6110 insertion within the TBD1 region.*
assembly/README.md 0 → 100644
+ 77
− 0
View file @ dbda4ecc
# Genome assembly workflow
The user needs to modify two things to run the workflow on her samples:
- the file config/samples.tsv, which contains the sample names and the corresponding paths to the HiFi consensus reads.
- the file config/config.yaml, which contains global options for the analysis
## container
Problem: 1.6 gb container on gitlab? Building or loading container requires sudo...
```
sudo singularity build assemblySMK.sif assemblySMK.def
```
## samples.tsv
This is a tab-separated table with a header and two colums (see example): the first containing the sample names, which will be used to name the assemblies; the second with the absolute paths to the fastq files.
## config.yaml
In the file config/config.yaml some global parameters can be set:
```yaml
samples: samples.inhouse.hifi.test.csv
results_directory: ./results
output_prefix: pb_bernese
ref:
genome_size: 4.4m
gbf: resources/H37Rv.gbf
threads: 4
keep_intermediate: "Yes"
```
## Dry-run
```
snakemake -n
```
## Run the workflow on scicore
Important: singularity containers most be given access to the file locations through the --bind argument. E.g. if the long reads are on /scicore/home/jean-jacques/reads/, add this location in the snakemake command (see also the full command below):
```
--singularity-args "--bind /scicore/home/jean-jacques/reads/"
```
It's convenient to run snakemake in a screen, so we can do other things on scicore while it's running and occasionally check the progress.
Important snakemake arguments:
--jobs:
--cluster
```
screen -r assembly
snakemake \
--jobs 4
-k \
--latency-wait 60 \
--use-singularity --singularity-args "--bind /scicore/home/gagneux/GROUP/tbresearch/genomes/IN_PROGRESS/PacBio_genomes/Gagneux --bind /scicore/home/gagneux/stritt0001/TB/projects/pacbio_microscale/ --bind /scratch" \
--cluster "sbatch --job-name=hifi_simul --cpus-per-task=4 --mem-per-cpu=4G --time=06:00:00 --qos=6hours --output=hifi_simul.o%j --error=hifi_simul.e%j"
```
Leave the screen with CTRL+a+d.
\ No newline at end of file
assembly/config.yaml 0 → 100755
+ 18
− 0
View file @ dbda4ecc
##############################
#
##############################
samples: samples.tsv
project_directory: ./results
output_prefix: pb_bernese
ref:
genome_size: 4.4m
gbf: resources/H37Rv.gbf
threads: 4
keep_intermediate: "Yes"
mapreads: "No"
assembly/container/README.md 0 → 100644
+ 49
− 0
View file @ dbda4ecc
Problem: 1.6 gb container on gitlab? Building or loading container requires sudo...
```
sudo singularity build assemblySC.sif assemblySC.def
```
# Create versioned direct file and locked dependency file (https://pythonspeed.com/articles/conda-dependency-management/)
environment.yml: versioned main dependencies
conda-lock.yml: locked subdependencies
```
conda create -n assemblySnake
conda activate assemblySnake
mamba install \
flye \
samtools \
minimap2 \
circlator \
panaroo \
prokka \
numpy \
scipy \
matplotlib \
scikit-learn \
pandas \
jinja2 \
h5py \
pysam \
edlib \
python-edlib \
biopython
conda env export --from-history > environment.yml # manually edit to keep main dependencies
# Update environment
conda env update --file environment.yml --prune
# Create locked version
conda-lock --mamba -f environment.yml -p linux-64
conda-lock render -p linux-64 # allows using mamba create --file conda-linux-64.lock
assembly/container/assemblySC.def 0 → 100644
+ 54
− 0
View file @ dbda4ecc
Bootstrap: docker
From: condaforge/mambaforge:23.1.0-1
%files
conda-linux-64.lock
%post
export PATH=/opt/conda/bin:$PATH
mamba create --name pb_assembly --file conda-linux-64.lock
mamba clean -afy
apt-get clean all
apt-get update
apt-get upgrade -y
apt-get install -y build-essential libc6-dev zlib1g-dev less
apt-get clean
apt-get purge
git clone --depth 1 https://github.com/yfukasawa/LongQC.git
cd LongQC/minimap2-coverage && make
# Install mash
apt-get install -y mash
# Install polypolish
wget https://github.com/rrwick/Polypolish/releases/download/v0.5.0/polypolish-linux-x86_64-musl-v0.5.0.tar.gz
tar -xf polypolish-linux-x86_64-musl-v0.5.0.tar.gz -C /opt/conda/bin
rm polypolish-linux-x86_64-musl-v0.5.0.tar.gz
# Install progressiveCactus
wget https://github.com/ComparativeGenomicsToolkit/cactus/releases/download/v2.6.0/cactus-bin-v2.6.0.tar.gz
tar -xf cactus-bin-v2.6.0.tar.gz -C /opt/conda/bin
rm cactus-bin-v2.6.0.tar.gz
# set to whatever your conda path is, I usually install to /opt
echo ". /opt/conda/etc/profile.d/conda.sh" >> $SINGULARITY_ENVIRONMENT
echo "conda activate pb_assembly" >> $SINGULARITY_ENVIRONMENT
%environment
export PATH="/opt/conda/bin:/usr/local/bin:/usr/bin:/bin:"
unset CONDA_DEFAULT_ENV
export ANACONDA_HOME=/opt/conda
export PATH=LongQC/minimap2-coverage:$PATH
%help
%runscript
exec /bin/bash "$@"
%startscript
exec /bin/bash "$@"
assembly/container/conda-linux-64.lock 0 → 100644
+ 372
− 0
View file @ dbda4ecc
# Generated by conda-lock.
# platform: linux-64
# input_hash: 182af84a8c8a1dc9eb2c6bdc76285050405b5c964d7feda7b0a4ea7d966f0976
@EXPLICIT
https://repo.anaconda.com/pkgs/main/linux-64/_libgcc_mutex-0.1-main.conda#c3473ff8bdb3d124ed5ff11ec380d6f9
https://repo.anaconda.com/pkgs/main/linux-64/blas-1.0-mkl.conda#9a7a051e9bd41da46523acb017d8a517
https://repo.anaconda.com/pkgs/main/linux-64/ca-certificates-2023.05.30-h06a4308_0.conda#979be8dd2368decd342b13e01540d297
https://repo.anaconda.com/pkgs/main/linux-64/ld_impl_linux-64-2.38-h1181459_1.conda#68eedfd9c06f2b0e6888d8db345b7f5b
https://repo.anaconda.com/pkgs/main/linux-64/libgfortran4-7.5.0-ha8ba4b0_17.conda#e3883581cbf0a98672250c3e80d292bf
https://repo.anaconda.com/pkgs/main/linux-64/openjdk-8.0.152-h7b6447c_3.conda#e3100a32e7741538a72196a721f988d9
https://repo.anaconda.com/pkgs/main/linux-64/libgfortran-ng-7.5.0-ha8ba4b0_17.conda#ecb35c8952579d5c8dc56c6e076ba948
https://repo.anaconda.com/pkgs/main/linux-64/libgomp-11.2.0-h1234567_1.conda#b372c0eea9b60732fdae4b817a63c8cd
https://repo.anaconda.com/pkgs/main/linux-64/libstdcxx-ng-11.2.0-h1234567_1.conda#57623d10a70e09e1d048c2b2b6f4e2dd
https://conda.anaconda.org/bioconda/noarch/minced-0.4.2-hdfd78af_1.tar.bz2#eee6ac504430c045623a6616e13ba833
https://repo.anaconda.com/pkgs/main/linux-64/_openmp_mutex-5.1-1_gnu.conda#71d281e9c2192cb3fa425655a8defb85
https://conda.anaconda.org/bioconda/linux-64/edlib-1.2.3-h2d50403_1.tar.bz2#d85cba3681b8c8b207d94f9f31737a39
https://repo.anaconda.com/pkgs/main/linux-64/libgcc-ng-11.2.0-h1234567_1.conda#a87728dabf3151fb9cfa990bd2eb0464
https://conda.anaconda.org/bioconda/linux-64/aragorn-1.2.41-hec16e2b_0.tar.bz2#35e36bf31751b11dda35afcc2d28f89b
https://repo.anaconda.com/pkgs/main/linux-64/bzip2-1.0.8-h7b6447c_0.conda#9303f4af7c004e069bae22bde8d800ee
https://conda.anaconda.org/bioconda/linux-64/clustalw-2.1-h9f5acd7_7.tar.bz2#f965c89e793fd85efcb7241d07042985
https://repo.anaconda.com/pkgs/main/linux-64/expat-2.2.10-he6710b0_2.conda#e8b086ca590c1bd0d2a709d3affbda48
https://repo.anaconda.com/pkgs/main/linux-64/fribidi-1.0.10-h7b6447c_0.conda#1b4851703971b3d43acdcc9c72777575
https://repo.anaconda.com/pkgs/main/linux-64/giflib-5.2.1-h5eee18b_3.conda#aa7d64adb3cd8a75d398167f8c29afc3
https://repo.anaconda.com/pkgs/main/linux-64/graphite2-1.3.14-h295c915_1.conda#1939e8b3c03da6de2c021bd41aead9f9
https://conda.anaconda.org/bioconda/linux-64/hmmer-3.3.2-h87f3376_2.tar.bz2#fefeadd4a743164946031ab491a347ab
https://repo.anaconda.com/pkgs/main/linux-64/icu-58.2-he6710b0_3.conda#48cc14d5ad1a9bcd8dac17211a8deb8b
https://conda.anaconda.org/bioconda/linux-64/infernal-1.1.4-h779adbc_0.tar.bz2#9f9f83d7e5e855d34af6876faf880167
https://repo.anaconda.com/pkgs/main/linux-64/jpeg-9e-h5eee18b_1.conda#ac373800fda872108412d1ccfe3fa572
https://repo.anaconda.com/pkgs/main/linux-64/libbrotlicommon-1.0.9-h5eee18b_7.conda#73357cb8fde4b92707ec575c8d8a7ebc
https://repo.anaconda.com/pkgs/main/linux-64/libdb-6.2.32-h6a678d5_1.conda#3f0e8b19439efa7dad29eb8f6586f09e
https://conda.anaconda.org/bioconda/linux-64/libdeflate-1.0-h14c3975_1.tar.bz2#6597b611d5070ad5fcef34a26a8065e3
https://repo.anaconda.com/pkgs/main/linux-64/libffi-3.2.1-hf484d3e_1007.conda#ef4c7b437f50a1ab4920dc313d8ebc28
https://repo.anaconda.com/pkgs/main/linux-64/libidn11-1.33-h7b6447c_0.conda#75d5c232628eb6701d7a491716243a1f
https://repo.anaconda.com/pkgs/main/linux-64/libunistring-0.9.10-h27cfd23_0.conda#5b6ed6cd1b1ca3a383daef1d6464d02a
https://repo.anaconda.com/pkgs/main/linux-64/libuuid-1.41.5-h5eee18b_0.conda#4a6a2354414c9080327274aa514e5299
https://repo.anaconda.com/pkgs/main/linux-64/libwebp-base-1.2.4-h5eee18b_1.conda#a65a20c48061ecf2a6f4f02eae9f2366
https://repo.anaconda.com/pkgs/main/linux-64/libxcb-1.15-h7f8727e_0.conda#ada518dcadd6aaee9aae47ba9a671553
https://repo.anaconda.com/pkgs/main/linux-64/lz4-c-1.9.4-h6a678d5_0.conda#53915e9402180a7f22ea619c41089520
https://conda.anaconda.org/bioconda/linux-64/mafft-7.505-hec16e2b_0.tar.bz2#33da74c785690ab510469051072d5a90
https://repo.anaconda.com/pkgs/main/linux-64/ncurses-6.1-he6710b0_1.conda#2ddad69032f38ace29c50b2ee7c5e080
https://repo.anaconda.com/pkgs/main/linux-64/openssl-1.1.1u-h7f8727e_0.conda#71334c111226af34891ad41811d962c3
https://conda.anaconda.org/bioconda/linux-64/paml-4.9-hec16e2b_7.tar.bz2#41888eb05cc9da15d9e2ef3bb6950f40
https://repo.anaconda.com/pkgs/main/linux-64/pcre-8.45-h295c915_0.conda#b32ccc24d1d9808618c1e898da60f68d
https://repo.anaconda.com/pkgs/main/linux-64/perl-5.26.2-h14c3975_0.conda#146f65488ff2239f08a9f98942b60e1c
https://repo.anaconda.com/pkgs/main/linux-64/pixman-0.40.0-h7f8727e_1.conda#406469dab3fdd6c24eae7dd18f649930
https://conda.anaconda.org/bioconda/linux-64/prodigal-2.6.3-hec16e2b_4.tar.bz2#0f8b880d727df321ac70a224c18690cb
https://repo.anaconda.com/pkgs/main/linux-64/tbb-2021.8.0-hdb19cb5_0.conda#869373905a6bfacbb967abc98516dd85
https://conda.anaconda.org/bioconda/linux-64/tidyp-1.04-hec16e2b_4.tar.bz2#d5b09ebf6f220ce63d2d1316ad58b596
https://repo.anaconda.com/pkgs/main/linux-64/xz-5.2.10-h5eee18b_1.conda#dd172c348274807ec0d841df8295b670
https://repo.anaconda.com/pkgs/main/linux-64/zlib-1.2.13-h5eee18b_0.conda#333e31fbfbb5057c92fa845ad6adef93
https://conda.anaconda.org/bioconda/linux-64/bedtools-2.30.0-h7d7f7ad_2.tar.bz2#7ae50bfa652342afa61ea0861c81074e
https://conda.anaconda.org/bioconda/linux-64/bwa-0.7.17-h5bf99c6_8.tar.bz2#296699e49a5c7d784cbe9dd788848fb5
https://conda.anaconda.org/bioconda/linux-64/cd-hit-4.8.1-h2e03b76_5.tar.bz2#1e14919732da571de7b77e2cbf36b551
https://repo.anaconda.com/pkgs/main/linux-64/glib-2.63.1-h5a9c865_0.conda#c05e1fa89ebacdd19c8ec896cfff59ed
https://repo.anaconda.com/pkgs/main/linux-64/hdf5-1.10.6-hb1b8bf9_0.conda#a496f7ed2cbb6fb069b005f4df3c0cff
https://repo.anaconda.com/pkgs/main/linux-64/intel-openmp-2022.1.0-h9e868ea_3769.conda#ee98f23e5f7ec758c9f1979f7d050a3d
https://conda.anaconda.org/bioconda/linux-64/k8-0.2.5-h9a82719_1.tar.bz2#8700d84f57171e0d92bb5e7178aca95c
https://repo.anaconda.com/pkgs/main/linux-64/libbrotlidec-1.0.9-h5eee18b_7.conda#5c31f3bd570dc4d7d799117c98aad6e3
https://repo.anaconda.com/pkgs/main/linux-64/libbrotlienc-1.0.9-h5eee18b_7.conda#289179174f1216582a949b528d8224af
https://repo.anaconda.com/pkgs/main/linux-64/libedit-3.1.20181209-hc058e9b_0.conda#594c05f769516b55c004eada4fc9ea74
https://repo.anaconda.com/pkgs/main/linux-64/libidn2-2.3.4-h5eee18b_0.conda#2bd46aa89ec576ad787afcdd93e5eafb
https://repo.anaconda.com/pkgs/main/linux-64/libllvm11-11.0.0-h3826bc1_1.conda#44c5950cfe7a87f93a9909f3027c4504
https://repo.anaconda.com/pkgs/main/linux-64/libpng-1.6.39-h5eee18b_0.conda#f6aee38184512eb05b06c2e94d39ab22
https://repo.anaconda.com/pkgs/main/linux-64/libssh2-1.10.0-h37d81fd_2.conda#0a9ab49b65e0adb587f4a164e3deecfb
https://repo.anaconda.com/pkgs/main/linux-64/libxml2-2.9.14-h74e7548_0.conda#2eafeb1cb5f00b034d150f3d70436e52
https://conda.anaconda.org/bioconda/linux-64/mummer-3.23-pl5262h1b792b2_12.tar.bz2#dbd3e608b87abb39bc4652e55034b908
https://conda.anaconda.org/bioconda/linux-64/perl-algorithm-diff-1.1903-pl526_2.tar.bz2#4599aed943b7e8538a6eab5a9ad3f49f
https://conda.anaconda.org/bioconda/linux-64/perl-algorithm-munkres-0.08-pl526_1.tar.bz2#6b6f07a137705b8a11321c5d4f16bf38
https://conda.anaconda.org/bioconda/linux-64/perl-app-cpanminus-1.7044-pl526_1.tar.bz2#dcd34d99b75ca3feb8af1623a3859b20
https://conda.anaconda.org/bioconda/linux-64/perl-appconfig-1.71-pl526_1.tar.bz2#ce249bab46455b131908aa356c4b1277
https://conda.anaconda.org/bioconda/linux-64/perl-autoloader-5.74-pl526_2.tar.bz2#2db8980e46dbcbba3ecf62932d512087
https://conda.anaconda.org/bioconda/linux-64/perl-base-2.23-pl526_1.tar.bz2#03db12873cdeb00d4e8d02bcbf583a04
https://conda.anaconda.org/bioconda/linux-64/perl-capture-tiny-0.48-pl526_0.tar.bz2#8909e30032cdecdf407dd2eae7aff9dc
https://conda.anaconda.org/bioconda/linux-64/perl-class-data-inheritable-0.08-pl526_1.tar.bz2#e14ddc69cf2040a5e6578639a3cd4aa4
https://conda.anaconda.org/bioconda/linux-64/perl-class-inspector-1.34-pl526_0.tar.bz2#b530f218de761899c4d63759eadf28fc
https://conda.anaconda.org/bioconda/linux-64/perl-class-method-modifiers-2.12-pl526_0.tar.bz2#e395ece7e67b0f5e7ea2b2c0c628f2d5
https://conda.anaconda.org/bioconda/linux-64/perl-common-sense-3.74-pl526_2.tar.bz2#66f1c27dc24f6fc5d76d25cd9771f043
https://conda.anaconda.org/bioconda/linux-64/perl-compress-raw-bzip2-2.087-pl526he1b5a44_0.tar.bz2#452ca14d71cd5973a6db6998b50f30e3
https://conda.anaconda.org/bioconda/linux-64/perl-compress-raw-zlib-2.087-pl526hc9558a2_0.tar.bz2#6a7842c318054b9110268696ce2fe7be
https://conda.anaconda.org/bioconda/linux-64/perl-constant-1.33-pl526_1.tar.bz2#5037eea2bb962fab567d2d5ea43bc81a
https://conda.anaconda.org/bioconda/linux-64/perl-convert-binary-c-0.78-pl526h6bb024c_3.tar.bz2#4d3b23d40c53d03e38d777ea0c9a547b
https://conda.anaconda.org/bioconda/linux-64/perl-convert-binhex-1.125-pl526_1.tar.bz2#20f7f2f9158b5996c64f5747dcb1dbf2
https://conda.anaconda.org/bioconda/linux-64/perl-crypt-rc4-2.02-pl526_1.tar.bz2#bf0de5b85cc536e1293f2fc551feeccc
https://conda.anaconda.org/bioconda/linux-64/perl-data-dumper-2.173-pl526_0.tar.bz2#8057e13103637c6e8700c652d1b83682
https://conda.anaconda.org/bioconda/linux-64/perl-date-format-2.30-pl526_2.tar.bz2#68604a936e3f5241c5299ef1b37725dd
https://conda.anaconda.org/bioconda/linux-64/perl-db-file-1.855-pl526h516909a_0.tar.bz2#a234abd4c1aa57ef1f52f9b2d9be9b2c
https://conda.anaconda.org/bioconda/linux-64/perl-dbi-1.642-pl526_0.tar.bz2#539e75cef138499a204431ae72f3ade7
https://conda.anaconda.org/bioconda/noarch/perl-devel-stacktrace-2.04-pl526_0.tar.bz2#c26d7ca3e81c27cf6b1883fc16bc98eb
https://conda.anaconda.org/bioconda/linux-64/perl-digest-hmac-1.03-pl526_3.tar.bz2#8034b317d96bf32090e66ab8c6db9671
https://conda.anaconda.org/bioconda/linux-64/perl-digest-md5-2.55-pl526_0.tar.bz2#c10e244cdea0a2556c4a72111fa6ed38
https://conda.anaconda.org/bioconda/linux-64/perl-digest-perl-md5-1.9-pl526_1.tar.bz2#58e8ad466a0e7315a10be866f16f7b7d
https://conda.anaconda.org/bioconda/linux-64/perl-digest-sha1-2.13-pl526h6bb024c_1.tar.bz2#34f08c9ebc82b9357ff1a89712407e10
https://conda.anaconda.org/bioconda/linux-64/perl-dynaloader-1.25-pl526_1.tar.bz2#f8ef9b13d527c472a2a33a9218043f47
https://conda.anaconda.org/bioconda/linux-64/perl-email-date-format-1.005-pl526_2.tar.bz2#7c2c2c488712dd3ae36a829a9db2e3cf
https://conda.anaconda.org/bioconda/linux-64/perl-error-0.17027-pl526_1.tar.bz2#24dfde22ba84dd06eacafb8cb6acc989
https://conda.anaconda.org/bioconda/linux-64/perl-exporter-5.72-pl526_1.tar.bz2#5ecf4d143181f4a4d71349811ea29177
https://conda.anaconda.org/bioconda/linux-64/perl-exporter-tiny-1.002001-pl526_0.tar.bz2#b84ce6dbb823c77ddba901d1083c2e84
https://conda.anaconda.org/bioconda/linux-64/perl-extutils-makemaker-7.36-pl526_1.tar.bz2#32d1b791177a614aeae12e67bca620b0
https://conda.anaconda.org/bioconda/linux-64/perl-file-slurp-tiny-0.004-pl526_1.tar.bz2#1cf79bd3a86d7dbc00837771705beea3
https://conda.anaconda.org/bioconda/linux-64/perl-file-sort-1.01-pl526_2.tar.bz2#8b11f3a3337a6eeb69bed51180038954
https://conda.anaconda.org/bioconda/linux-64/perl-file-which-1.23-pl526_0.tar.bz2#46f24942ce35bdd275f905cfe93ac9e0
https://conda.anaconda.org/bioconda/linux-64/perl-font-afm-1.20-pl526_2.tar.bz2#abb160a30f5f6fd49ab1f5c9fcc6491e
https://conda.anaconda.org/bioconda/linux-64/perl-getopt-long-2.50-pl526_1.tar.bz2#3f11f5bb4d7fb82920bf1ffac2e49a0a
https://conda.anaconda.org/bioconda/linux-64/perl-graph-0.9704-pl526_1.tar.bz2#a65ac27d38caa1c9b9a9c50e57a7506e
https://conda.anaconda.org/bioconda/linux-64/perl-html-entities-numbered-0.04-pl526_1.tar.bz2#b94f3da1695f22440f7e6cbc3ccfff7a
https://conda.anaconda.org/bioconda/linux-64/perl-html-tagset-3.20-pl526_3.tar.bz2#169010ee892bae283dc8ae4c37ad268b
https://conda.anaconda.org/bioconda/linux-64/perl-image-size-3.300-pl526_2.tar.bz2#4fde2f534700c5db586857c1cb54a7fb
https://conda.anaconda.org/bioconda/linux-64/perl-io-html-1.001-pl526_2.tar.bz2#64455bdee28a81f80825a314a4044061
https://conda.anaconda.org/bioconda/linux-64/perl-io-sessiondata-1.03-pl526_1.tar.bz2#05a48ef984c5cd7d26f9a9f2cf6d2c4f
https://conda.anaconda.org/bioconda/linux-64/perl-io-string-1.08-pl526_3.tar.bz2#dad994f13fb037903c02f26b7ad3c63b
https://conda.anaconda.org/bioconda/linux-64/perl-io-stringy-2.111-pl526_1.tar.bz2#33ef4f37303997cd575f99337d50bf29
https://conda.anaconda.org/bioconda/linux-64/perl-io-tty-1.12-pl526_1.tar.bz2#a7a3013cf647487be217fa66d897430e
https://conda.anaconda.org/bioconda/linux-64/perl-io-zlib-1.10-pl526_2.tar.bz2#14acb0318f4ad06603b5d38706ae043a
https://conda.anaconda.org/bioconda/linux-64/perl-ipc-sharelite-0.17-pl526h6bb024c_1.tar.bz2#b0aff1dbd06425229a77a1835a1e2fde
https://conda.anaconda.org/bioconda/linux-64/perl-jcode-2.07-pl526_2.tar.bz2#4c1c173719e0f29cca3f17ae9eeb92ab
https://conda.anaconda.org/bioconda/linux-64/perl-lib-0.63-pl526_1.tar.bz2#03381abd528ca5beab93d60bc93106d0
https://conda.anaconda.org/bioconda/linux-64/perl-math-cdf-0.1-pl526h14c3975_5.tar.bz2#0f96fd4f8528a673b2b7acf152745f39
https://conda.anaconda.org/bioconda/linux-64/perl-math-derivative-1.01-pl526_0.tar.bz2#5c33680301345795f36e328ab1326c92
https://conda.anaconda.org/bioconda/linux-64/perl-math-random-0.72-pl526h14c3975_2.tar.bz2#f243daa84687810c0d966295691f9a33
https://conda.anaconda.org/bioconda/linux-64/perl-mime-types-2.17-pl526_0.tar.bz2#a2b8a924ddd48c80098dcbc31f3fd789
https://conda.anaconda.org/bioconda/linux-64/perl-mldbm-2.05-pl526_1.tar.bz2#57b7a95f18db31d9a14be8821d78fb1c
https://conda.anaconda.org/bioconda/linux-64/perl-module-runtime-0.016-pl526_1.tar.bz2#e700baa2ca15df31a85a13626a37ad5b
https://conda.anaconda.org/bioconda/linux-64/perl-mozilla-ca-20180117-pl526_1.tar.bz2#33c797816376ee2a58fd4187848ced82
https://conda.anaconda.org/bioconda/linux-64/perl-mro-compat-0.13-pl526_0.tar.bz2#1a374860fe4735444128341b386b0661
https://conda.anaconda.org/bioconda/linux-64/perl-ole-storage_lite-0.19-pl526_3.tar.bz2#756163b36016abb477b2c9e711096f41
https://conda.anaconda.org/bioconda/linux-64/perl-params-util-1.07-pl526h6bb024c_4.tar.bz2#68de50e31b49b11e3c0041ce1f377adb
https://conda.anaconda.org/bioconda/linux-64/perl-parent-0.236-pl526_1.tar.bz2#389bb45e15d386db8e32613a2eb2e949
https://conda.anaconda.org/bioconda/linux-64/perl-parse-recdescent-1.967015-pl526_0.tar.bz2#433ebb11e56c7ef98a97b282838d0ba1
https://conda.anaconda.org/bioconda/linux-64/perl-postscript-0.06-pl526_2.tar.bz2#0275574a4df776cac13dec7b312a5b07
https://conda.anaconda.org/bioconda/linux-64/perl-scalar-list-utils-1.52-pl526h516909a_0.tar.bz2#8c78fca5814513924f9637a9211c0c77
https://conda.anaconda.org/bioconda/linux-64/perl-set-scalar-1.29-pl526_2.tar.bz2#2beb1c6e6ad43af7272c343e79338597
https://conda.anaconda.org/bioconda/linux-64/perl-socket-2.027-pl526_1.tar.bz2#bbce777723970c529b99e0beaa09ec1c
https://conda.anaconda.org/bioconda/linux-64/perl-sort-naturally-1.03-pl526_2.tar.bz2#fba3b30a0be6d23e9ba4ecb78545656d
https://conda.anaconda.org/bioconda/linux-64/perl-sub-exporter-progressive-0.001013-pl526_0.tar.bz2#4567f34432f3ef33788f1b36d0ba41e9
https://conda.anaconda.org/bioconda/linux-64/perl-sub-identify-0.14-pl526h14c3975_0.tar.bz2#17126c427ca6c885ce4836d69f3f4825
https://conda.anaconda.org/bioconda/linux-64/perl-sub-name-0.21-pl526_1.tar.bz2#21286d90bd5855726fdbf1c92c35ca8b
https://conda.anaconda.org/bioconda/linux-64/perl-sub-quote-2.006003-pl526_1.tar.bz2#68a77efdc965c77669e4cf24659a4c64
https://conda.anaconda.org/bioconda/linux-64/perl-sub-uplevel-0.2800-pl526h14c3975_2.tar.bz2#86e5aa3c24a698f26a5200dd5c39cf44
https://conda.anaconda.org/bioconda/linux-64/perl-svg-2.84-pl526_0.tar.bz2#88999f93f550ed7f4766f39c7616c1c3
https://conda.anaconda.org/bioconda/linux-64/perl-task-weaken-1.06-pl526_0.tar.bz2#9aa2fd2dae5a9e0adcd99ff8deade351
https://conda.anaconda.org/bioconda/linux-64/perl-test-deep-1.128-pl526_1.tar.bz2#463602fbe90af90f16b75abebced5bd1
https://conda.anaconda.org/bioconda/linux-64/perl-test-harness-3.42-pl526_0.tar.bz2#5a82f26d026ea1dec91ceb9d0ab55b21
https://conda.anaconda.org/bioconda/linux-64/perl-test-leaktrace-0.16-pl526h14c3975_2.tar.bz2#7fe075d24f9517b9f3a12402f16634af
https://conda.anaconda.org/bioconda/noarch/perl-threaded-5.32.1-hdfd78af_1.tar.bz2#7ec21ca86ddac0449501c2463370b714
https://conda.anaconda.org/bioconda/linux-64/perl-tie-ixhash-1.23-pl526_2.tar.bz2#285e63900d249ff468ea55603769a99d
https://conda.anaconda.org/bioconda/linux-64/perl-timedate-2.30-pl526_1.tar.bz2#8d00993e312e67b62a253ed3b2ee0360
https://conda.anaconda.org/bioconda/linux-64/perl-try-tiny-0.30-pl526_1.tar.bz2#cf04b17e5804be0615363036e37b9ca7
https://conda.anaconda.org/bioconda/linux-64/perl-unicode-map-0.112-pl526h6bb024c_3.tar.bz2#da4af750734feda730d4ec28ce40d9f9
https://conda.anaconda.org/bioconda/linux-64/perl-xml-parser-2.44-pl526h4e0c4b3_7.tar.bz2#5cac1a41d5233b035b11d9099047027e
https://conda.anaconda.org/bioconda/linux-64/perl-xml-regexp-0.04-pl526_2.tar.bz2#622610ae70881fc769fae6c71e95d979
https://conda.anaconda.org/bioconda/linux-64/perl-xml-sax-base-1.09-pl526_0.tar.bz2#1a66227c893c9aa02e442019f8052374
https://conda.anaconda.org/bioconda/linux-64/perl-xml-writer-0.625-pl526_2.tar.bz2#b1d6525412fa858a778c6d72b8c62fb8
https://conda.anaconda.org/bioconda/linux-64/perl-xml-xpathengine-0.14-pl526_2.tar.bz2#d268cc26d463321abc01f107beaf2553
https://conda.anaconda.org/bioconda/linux-64/perl-xsloader-0.24-pl526_0.tar.bz2#878d48f2a6bdff58c7b9589e3b25ff6b
https://conda.anaconda.org/bioconda/noarch/perl-yaml-1.29-pl526_0.tar.bz2#9bf9b027106526977ff3efe2032c3ae5
https://repo.anaconda.com/pkgs/main/linux-64/readline-7.0-h7b6447c_5.conda#a710317bab8ee910a028ddf6da64158b
https://conda.anaconda.org/bioconda/linux-64/tbl2asn-25.7-h9ee0642_1.tar.bz2#058e9e623ffa3067dc1879774c4520e4
https://repo.anaconda.com/pkgs/main/linux-64/tk-8.6.12-h1ccaba5_0.conda#fa10ff4aa631fa4aa090a6234d7770b9
https://repo.anaconda.com/pkgs/main/linux-64/zstd-1.5.5-hc292b87_0.conda#0f59d57dc21f585f4c282d60dfb46505
https://conda.anaconda.org/bioconda/noarch/barrnap-0.9-hdfd78af_4.tar.bz2#da96203ff6df1a221c22dfde37951bdf
https://repo.anaconda.com/pkgs/main/linux-64/brotli-bin-1.0.9-h5eee18b_7.conda#1cc9b5d3edf7bf3247941f4b5c083242
https://repo.anaconda.com/pkgs/main/linux-64/dbus-1.13.18-hb2f20db_0.conda#6a6a6f1391f807847404344489ef6cf4
https://repo.anaconda.com/pkgs/main/linux-64/freetype-2.12.1-h4a9f257_0.conda#bdc7b5952e9c5dca01bc2f4ccef2f974
https://repo.anaconda.com/pkgs/main/linux-64/gstreamer-1.14.0-hb453b48_1.conda#e9b8ad6885e6a342de09c9168bf30e8a
https://repo.anaconda.com/pkgs/main/linux-64/krb5-1.17.1-h173b8e3_0.conda#d1de8847d71a7549b0b1a0b3cc51f8eb
https://repo.anaconda.com/pkgs/main/linux-64/libtiff-4.2.0-hecacb30_2.conda#075965745767d510e794b0d1188b90c9
https://repo.anaconda.com/pkgs/main/linux-64/libxslt-1.1.35-h4e12654_0.conda#328c111d87dccd5a3e471a691833f670
https://conda.anaconda.org/bioconda/linux-64/minimap2-2.22-h5bf99c6_0.tar.bz2#04f620368bd69606d3b7abc45281fda2
https://repo.anaconda.com/pkgs/main/linux-64/mkl-2019.4-243.conda#25511101129b3e0edda105b192b2d56d
https://conda.anaconda.org/bioconda/linux-64/parallel-20160622-1.tar.bz2#c1d15f62f1f2fb792de309b87538de17
https://conda.anaconda.org/bioconda/linux-64/perl-carp-1.38-pl526_3.tar.bz2#984c76663b1bd6e880683ce6fa58da4c
https://conda.anaconda.org/bioconda/linux-64/perl-clone-0.42-pl526h516909a_0.tar.bz2#2a940c5eac2973934e3d2b7d7da2a42c
https://conda.anaconda.org/bioconda/linux-64/perl-dbd-sqlite-1.64-pl526h516909a_0.tar.bz2#e174559d63638b9b1ff18e063f0b3173
https://conda.anaconda.org/bioconda/linux-64/perl-devel-globaldestruction-0.14-pl526_0.tar.bz2#69d6adc91ae0495db3f7b1641a62fe72
https://conda.anaconda.org/bioconda/linux-64/perl-encode-2.88-pl526_1.tar.bz2#0db0d9088045596254fb8a88a9a37294
https://conda.anaconda.org/bioconda/linux-64/perl-exception-class-1.44-pl526_0.tar.bz2#0ad1976b098896c3914c4b6a71b2cc29
https://conda.anaconda.org/bioconda/linux-64/perl-file-path-2.16-pl526_0.tar.bz2#c58f86c77e01c9c62415ba917f7b651e
https://conda.anaconda.org/bioconda/linux-64/perl-font-ttf-1.06-pl526_0.tar.bz2#27f80e8d4202b360fbb0646fa31ee101
https://conda.anaconda.org/bioconda/linux-64/perl-html-parser-3.72-pl526h6bb024c_5.tar.bz2#9874aecaa5a6f19c55f32baa5cc7302e
https://conda.anaconda.org/bioconda/linux-64/perl-io-compress-2.087-pl526he1b5a44_0.tar.bz2#67679464cddb80ccc4692c6d76a439d5
https://conda.anaconda.org/bioconda/linux-64/perl-ipc-run-20180523.0-pl526_0.tar.bz2#8c4578f521fdeb854012141a98295526
https://conda.anaconda.org/bioconda/linux-64/perl-libxml-perl-0.08-pl526_2.tar.bz2#88024a4f468f99a79db70e461e546f84
https://conda.anaconda.org/bioconda/linux-64/perl-list-moreutils-xs-0.428-pl526_0.tar.bz2#65212b0ac443324d61e649d1752947c7
https://conda.anaconda.org/bioconda/noarch/perl-mailtools-2.21-pl526_0.tar.bz2#2e44b03f9ec0c8ab35f01612861f73da
https://conda.anaconda.org/bioconda/linux-64/perl-math-spline-0.02-pl526_2.tar.bz2#0981985687a311d7d2a0ad8551ae48fd
https://conda.anaconda.org/bioconda/linux-64/perl-mime-base64-3.15-pl526_1.tar.bz2#6ebc750ac3e57ca1f02d3f580ff281b3
https://conda.anaconda.org/bioconda/linux-64/perl-ntlm-1.09-pl526_4.tar.bz2#7863718bc88444211e686dc91dbf4292
https://conda.anaconda.org/bioconda/linux-64/perl-package-stash-xs-0.28-pl526hf484d3e_1.tar.bz2#38303819167b4ba65386a85f88a997a8
https://conda.anaconda.org/bioconda/linux-64/perl-pod-escapes-1.07-pl526_1.tar.bz2#e742de28b39935198dd942aae04335ea
https://conda.anaconda.org/bioconda/noarch/perl-role-tiny-2.000008-pl526_0.tar.bz2#ac07880e4a117a8c96b3eaf0dd545d40
https://conda.anaconda.org/bioconda/linux-64/perl-spreadsheet-writeexcel-2.40-pl526_2.tar.bz2#dbc71d9bfe4d0e81e9f1f36132728147
https://conda.anaconda.org/bioconda/linux-64/perl-storable-3.15-pl526h14c3975_0.tar.bz2#ad27b25076f3d76c10085d900bdf3a48
https://conda.anaconda.org/bioconda/linux-64/perl-test-1.26-pl526_1.tar.bz2#0d04bf8c5cde9cae87d9892633f0c17e
https://conda.anaconda.org/bioconda/linux-64/perl-test-exception-0.43-pl526_2.tar.bz2#245bc80913f1725d4aff7c12bb217d12
https://conda.anaconda.org/bioconda/linux-64/perl-test-requiresinternet-0.05-pl526_0.tar.bz2#47a9cfbedd72952aa493625692404a4e
https://conda.anaconda.org/bioconda/linux-64/perl-test-warn-0.36-pl526_1.tar.bz2#8805c991e44c05dd27e1c57aa86ed570
https://conda.anaconda.org/bioconda/linux-64/perl-text-diff-1.45-pl526_0.tar.bz2#98e32f19827755284e6d6e4c100b4108
https://conda.anaconda.org/bioconda/linux-64/perl-tree-dag_node-1.31-pl526_0.tar.bz2#de7717434961887f9c2cc16e7bd4e113
https://conda.anaconda.org/bioconda/linux-64/perl-type-tiny-1.004004-pl526_0.tar.bz2#5964382cfe9204ad562899023b7d559e
https://conda.anaconda.org/bioconda/linux-64/perl-types-serialiser-1.0-pl526_2.tar.bz2#77250c3feefab1e4a8f0fd482af07048
https://conda.anaconda.org/bioconda/linux-64/perl-xml-filter-buffertext-1.01-pl526_2.tar.bz2#b24d93bb57d72099dbaae9b7d442f932
https://conda.anaconda.org/bioconda/linux-64/perl-xml-namespacesupport-1.12-pl526_0.tar.bz2#14a68d6d3f08c2d64284919697a2a7ae
https://conda.anaconda.org/bioconda/linux-64/perl-xml-xpath-1.44-pl526_0.tar.bz2#166779d5aaca0eaf3074430e1afc4ebe
https://repo.anaconda.com/pkgs/main/linux-64/sqlite-3.31.1-h7b6447c_0.conda#c2cae59a837775a03aed11469994981c
https://repo.anaconda.com/pkgs/main/linux-64/wget-1.21.4-h91b91d3_1.conda#aff9953ea8a591b8c3c50bf0e55ed9ab
https://repo.anaconda.com/pkgs/main/linux-64/brotli-1.0.9-h5eee18b_7.conda#fb777289bceecf617ca9e35dd4484c86
https://conda.anaconda.org/bioconda/linux-64/entrez-direct-16.2-he881be0_1.tar.bz2#ff30142050ba583481215a6e1b3a5de0
https://repo.anaconda.com/pkgs/main/linux-64/fontconfig-2.14.1-hef1e5e3_0.conda#ade72b21d7ef60f012c3ca269a3e267e
https://repo.anaconda.com/pkgs/main/linux-64/gst-plugins-base-1.14.0-hbbd80ab_1.conda#4461ffa28478fe3ca9d0bea4e3395ed8
https://repo.anaconda.com/pkgs/main/linux-64/lcms2-2.12-h3be6417_0.conda#719db47afba9f6586eecb5eacac70bff
https://repo.anaconda.com/pkgs/main/linux-64/libcurl-7.69.1-h20c2e04_0.conda#ff0002442c81432f88280f8bd39731f4
https://repo.anaconda.com/pkgs/main/linux-64/libwebp-1.2.4-h11a3e52_1.conda#9f9153b30e58e9ce896f74634622cbf1
https://conda.anaconda.org/bioconda/linux-64/perl-business-isbn-data-20140910.003-pl526_0.tar.bz2#a3388b8a93d46fd71c88675528c11570
https://conda.anaconda.org/bioconda/linux-64/perl-cache-cache-1.08-pl526_0.tar.bz2#595971547a722e805a9bc0f9f1979995
https://conda.anaconda.org/bioconda/linux-64/perl-dist-checkconflicts-0.11-pl526_2.tar.bz2#f3af49e2ec0ebc45c8eeed12212a295f
https://conda.anaconda.org/bioconda/linux-64/perl-encode-locale-1.05-pl526_6.tar.bz2#8b76e07f2ee0eb2a4429e517f1ae0bbd
https://conda.anaconda.org/bioconda/linux-64/perl-eval-closure-0.14-pl526h6bb024c_4.tar.bz2#156f357c5abfa8690d8591ac8724235b
https://conda.anaconda.org/bioconda/linux-64/perl-file-temp-0.2304-pl526_2.tar.bz2#1e7930ea1b3a6d93a55c6b316a60a891
https://conda.anaconda.org/bioconda/linux-64/perl-html-tidy-1.60-pl526_0.tar.bz2#17c81b9261089410fb17206b7998a2af
https://conda.anaconda.org/bioconda/linux-64/perl-html-tree-5.07-pl526_1.tar.bz2#ea8d27cb7cfc1a14cc6d168e2f394dec
https://conda.anaconda.org/bioconda/linux-64/perl-json-xs-2.34-pl526h6bb024c_3.tar.bz2#3a5b157d275eae1d3ba16de1ccae8241
https://conda.anaconda.org/bioconda/linux-64/perl-list-moreutils-0.428-pl526_1.tar.bz2#699e3399479d2b1aa1f675b476406e0d
https://conda.anaconda.org/bioconda/linux-64/perl-lwp-mediatypes-6.04-pl526_0.tar.bz2#39688aa6f280b77af17f539350fe1744
https://conda.anaconda.org/bioconda/linux-64/perl-mime-lite-3.030-pl526_1.tar.bz2#4496ad7bf37b103f30e600e9d263e4b1
https://conda.anaconda.org/bioconda/linux-64/perl-mime-tools-5.508-pl526_1.tar.bz2#203ba9f173d1835bab0115af8f0d142e
https://conda.anaconda.org/bioconda/linux-64/perl-module-implementation-0.09-pl526_2.tar.bz2#97f9a0c37978d25299f4f1434c7a12e9
https://conda.anaconda.org/bioconda/linux-64/perl-net-ssleay-1.88-pl526h90d6eec_0.tar.bz2#8b541f03a7629fd90f71a797599b6c51
https://conda.anaconda.org/bioconda/linux-64/perl-pathtools-3.75-pl526h14c3975_1.tar.bz2#4ac5eb7fe5450b7a28c9dc5423c7c293
https://conda.anaconda.org/bioconda/noarch/perl-pdf-api2-2.035-pl526_0.tar.bz2#e0ded5596488cddcf789cef00409eaf7
https://conda.anaconda.org/bioconda/linux-64/perl-pod-usage-1.69-pl526_1.tar.bz2#7b9be57b2eb879efe65d7672d35d630c
https://conda.anaconda.org/bioconda/linux-64/perl-spreadsheet-parseexcel-0.65-pl526_2.tar.bz2#b703e8b5c2f2ef3bcf0816a628e56211
https://conda.anaconda.org/bioconda/linux-64/perl-sub-install-0.928-pl526_2.tar.bz2#90f883f49150f297aa62f231e989ef45
https://conda.anaconda.org/bioconda/noarch/perl-test-differences-0.67-pl526_0.tar.bz2#256f0110145fa69a7c0ccf41a993fae5
https://conda.anaconda.org/bioconda/linux-64/perl-time-hires-1.9760-pl526h14c3975_1.tar.bz2#dbbf8390d9c47e977f57c29b04391101
https://conda.anaconda.org/bioconda/linux-64/perl-time-local-1.28-pl526_1.tar.bz2#d24b02d0c1a45310c46fb48c691f51ce
https://conda.anaconda.org/bioconda/linux-64/perl-xml-sax-writer-0.57-pl526_0.tar.bz2#cf16306ca30b6099dc0e39edd9587b4a
https://repo.anaconda.com/pkgs/main/linux-64/python-3.7.6-h0371630_2.conda#dd58091b9580c94b09c05fa0b11d5285
https://repo.anaconda.com/pkgs/main/linux-64/argh-0.26.2-py37_0.conda#f9c42e754719f59f4024bbe56708b1d5
https://repo.anaconda.com/pkgs/main/linux-64/cairo-1.14.12-h8948797_3.conda#3436994526c285053941c46049cd943c
https://repo.anaconda.com/pkgs/main/linux-64/certifi-2022.12.7-py37h06a4308_0.conda#f71525bff3708b8c6232bd7535c032ca
https://repo.anaconda.com/pkgs/main/linux-64/curl-7.69.1-hbc83047_0.conda#0478de4737cfe1095fc6a4fe4a58d824
https://repo.anaconda.com/pkgs/main/noarch/cycler-0.11.0-pyhd3eb1b0_0.conda#f5e365d2cdb66d547eb8c3ab93843aab
https://conda.anaconda.org/bioconda/noarch/dendropy-4.6.1-pyhdfd78af_0.tar.bz2#e6f709c0a6e678d1a7566c8e1828a199
https://repo.anaconda.com/pkgs/main/linux-64/et_xmlfile-1.1.0-py37h06a4308_0.conda#2140b24ca3c4c243f43de1de7f134159
https://repo.anaconda.com/pkgs/main/noarch/flit-core-3.6.0-pyhd3eb1b0_0.conda#76802308ba7ec348cf0ca100cb133e67
https://repo.anaconda.com/pkgs/main/linux-64/joblib-1.1.1-py37h06a4308_0.conda#c54f1f11e171665b9b126334fb49eab3
https://repo.anaconda.com/pkgs/main/linux-64/libgd-2.3.3-h695aa2c_1.conda#a83694f90f2668f9e94ff0c78a8c5209
https://repo.anaconda.com/pkgs/main/linux-64/llvmlite-0.37.0-py37h295c915_2.conda#8889849fa382a96cf247e0326bb3b855
https://repo.anaconda.com/pkgs/main/linux-64/markupsafe-2.1.1-py37h7f8727e_0.conda#5785bf25230132d5de68de496d74e6c4
https://conda.anaconda.org/bioconda/noarch/munkres-1.0.7-py_1.tar.bz2#783d3baa1b57281daf35ce2a07a86017
https://repo.anaconda.com/pkgs/main/noarch/networkx-2.6.3-pyhd3eb1b0_0.conda#9b21e21dc3151fbe0e283ce752601dc3
https://repo.anaconda.com/pkgs/main/linux-64/packaging-22.0-py37h06a4308_0.conda#74d6ef6fbc69680d883cce4b3288d9f6
https://conda.anaconda.org/bioconda/linux-64/perl-aceperl-1.92-pl526_2.tar.bz2#8f0932e2e264bebf85619c4ef2f166a8
https://conda.anaconda.org/bioconda/linux-64/perl-apache-test-1.40-pl526_1.tar.bz2#c2f127c5de6f8fa7ae28fe2ac9b80b2f
https://conda.anaconda.org/bioconda/linux-64/perl-archive-tar-2.32-pl526_0.tar.bz2#961b7fd4f58d59d7d4f9f3e48f679477
https://conda.anaconda.org/bioconda/linux-64/perl-business-isbn-3.004-pl526_0.tar.bz2#982a9766a06c69ce335cbd8567e98e7a
https://conda.anaconda.org/bioconda/linux-64/perl-cgi-4.44-pl526h14c3975_1.tar.bz2#abf86df04595969e49c5ac3f295e2a20
https://conda.anaconda.org/bioconda/linux-64/perl-data-optlist-0.110-pl526_2.tar.bz2#75fa30de8891608438299a6f66c34014
https://conda.anaconda.org/bioconda/linux-64/perl-html-element-extended-1.18-pl526_1.tar.bz2#669cd8a0267b07a854c500c253313485
https://conda.anaconda.org/bioconda/linux-64/perl-html-formatter-2.16-pl526_0.tar.bz2#d6b3ce13b92712f81096c89ea8f454d3
https://conda.anaconda.org/bioconda/linux-64/perl-html-treebuilder-xpath-0.14-pl526_1.tar.bz2#55bd49ac3c4c1da46d5c0721ca3c9315
https://conda.anaconda.org/bioconda/linux-64/perl-http-date-6.02-pl526_3.tar.bz2#b1cc187d512357b0a68dc29a100ae1df
https://conda.anaconda.org/bioconda/linux-64/perl-io-socket-ssl-2.066-pl526_0.tar.bz2#16748c0ece26b643c259805c188b4114
https://conda.anaconda.org/bioconda/linux-64/perl-json-4.02-pl526_0.tar.bz2#14082a3e2b78deb9aa3ca880ab9eb854
https://conda.anaconda.org/bioconda/linux-64/perl-lwp-simple-6.15-pl526h470a237_4.tar.bz2#317554602ab7c16820944e7d75b36dd0
https://conda.anaconda.org/bioconda/linux-64/perl-module-runtime-conflicts-0.003-pl526_0.tar.bz2#b8eb3619137af69458c36fdc79b6a129
https://conda.anaconda.org/bioconda/linux-64/perl-statistics-descriptive-3.0702-pl526_0.tar.bz2#d30fe55f90cc24a85fa9a89a0a94c7b0
https://conda.anaconda.org/bioconda/linux-64/perl-test-most-0.35-pl526_0.tar.bz2#19ec7be21e08029005c2ff33b67c483f
https://conda.anaconda.org/bioconda/noarch/perl-xml-sax-1.02-pl526_0.tar.bz2#b4fda7e83376806d5eedbef2c3a3b356
https://repo.anaconda.com/pkgs/main/linux-64/pillow-9.4.0-py37h6a678d5_0.conda#ff8d322cc4dc1a5d6e60632598ee86ef
https://conda.anaconda.org/bioconda/noarch/pilon-1.24-hdfd78af_0.tar.bz2#4eef0c771dd3f81effb0d21ba8bb6734
https://conda.anaconda.org/bioconda/noarch/pyfastaq-3.17.0-py_2.tar.bz2#e29b1d017dcd935969a388130335bfa6
https://repo.anaconda.com/pkgs/main/linux-64/pyparsing-3.0.9-py37h06a4308_0.conda#853104fc62713a3c01eeef2b1c276264
https://conda.anaconda.org/bioconda/linux-64/python-edlib-1.3.8.post1-py37hc9558a2_0.tar.bz2#d540e9ecd93689ab23143b8c1fddebdf
https://repo.anaconda.com/pkgs/main/linux-64/pytz-2022.7-py37h06a4308_0.conda#36f0f56591c619474740299e08bd0e87
https://conda.anaconda.org/bioconda/noarch/pyvcf3-1.0.3-pyhdfd78af_0.tar.bz2#2471bf4fad9f15602ad24164adf1a22a
https://repo.anaconda.com/pkgs/main/linux-64/qt-5.9.7-h5867ecd_1.conda#05507dbc35c46ac5a7066fc860a62341
https://repo.anaconda.com/pkgs/main/linux-64/simplejson-3.17.6-py37h7f8727e_0.conda#a03e087c58c4385f2d89e0a9584e64f7
https://repo.anaconda.com/pkgs/main/linux-64/sip-4.19.8-py37hf484d3e_0.conda#a41603290a87146546d40828e3a3848d
https://repo.anaconda.com/pkgs/main/noarch/six-1.16.0-pyhd3eb1b0_1.conda#34586824d411d36af2fa40e799c172d0
https://conda.anaconda.org/bioconda/linux-64/spades-3.13.1-0.tar.bz2#b38542edf86af81067f2a519e2d21abe
https://repo.anaconda.com/pkgs/main/linux-64/tenacity-8.0.1-py37h06a4308_1.conda#d10d38eda7969473131e8529956913a2
https://repo.anaconda.com/pkgs/main/noarch/threadpoolctl-2.2.0-pyh0d69192_0.conda#bbfdbae4934150b902f97daaf287efe2
https://repo.anaconda.com/pkgs/main/linux-64/tornado-6.2-py37h5eee18b_0.conda#e88d10f78e1871494207a40642535518
https://repo.anaconda.com/pkgs/main/linux-64/tqdm-4.64.1-py37h06a4308_0.conda#4ce539dcc5028e5d8dbaeb8ea593b9b0
https://repo.anaconda.com/pkgs/main/linux-64/zipp-3.11.0-py37h06a4308_0.conda#0d442dcf71f352d8c5097a811b5daad5
https://conda.anaconda.org/bioconda/linux-64/blast-2.9.0-pl526he19e7b1_5.tar.bz2#48d145ee428832b095ee9810bcd0853b
https://repo.anaconda.com/pkgs/main/noarch/fonttools-4.25.0-pyhd3eb1b0_0.conda#bb9c5b5a6d892fca5efe4bf0203b6a48
https://repo.anaconda.com/pkgs/main/linux-64/harfbuzz-1.8.8-hffaf4a1_0.conda#ed3697c63497f052a0c7b66f9155ed60
https://conda.anaconda.org/bioconda/linux-64/htslib-1.9-ha228f0b_7.tar.bz2#9a8e267aa4a8d0de90929e664e8470cd
https://repo.anaconda.com/pkgs/main/linux-64/jinja2-3.1.2-py37h06a4308_0.conda#5150b8d17bbee948836922251a8e6a55
https://repo.anaconda.com/pkgs/main/linux-64/mkl-service-2.3.0-py37he8ac12f_0.conda#22fa74dfc830fd037481f883d7e9c1e2
https://repo.anaconda.com/pkgs/main/linux-64/openpyxl-3.0.10-py37h5eee18b_0.conda#d9fb6f80ad03756a2c285a30481dbd57
https://conda.anaconda.org/bioconda/linux-64/perl-file-listing-6.04-pl526_1.tar.bz2#2a2f44c2b29a326f46abb72aea331845
https://conda.anaconda.org/bioconda/linux-64/perl-gd-2.68-pl526he941832_0.tar.bz2#f2386e6cdbe8b93a6ac2f8e6dd6b8ec9
https://conda.anaconda.org/bioconda/linux-64/perl-html-tableextract-2.13-pl526_2.tar.bz2#ce74a864c8e3af76921cb8645372de61
https://conda.anaconda.org/bioconda/linux-64/perl-package-stash-0.38-pl526hf484d3e_1.tar.bz2#cfceef3c9c95da229cccb715ddd11c18
https://conda.anaconda.org/bioconda/linux-64/perl-sub-exporter-0.987-pl526_2.tar.bz2#5c47be06a5776fa6f3b6fb4e799bc5a1
https://conda.anaconda.org/bioconda/linux-64/perl-svg-graph-0.02-pl526_3.tar.bz2#1463029642c6a4fdfda96965698088f1
https://conda.anaconda.org/bioconda/linux-64/perl-uri-1.76-pl526_0.tar.bz2#30afcde2552ea47cdb5420e5319f66ad
https://conda.anaconda.org/bioconda/linux-64/perl-xml-libxml-2.0132-pl526h7ec2d77_1.tar.bz2#a9501a6119c0b10f7d20e6d3c15f9714
https://conda.anaconda.org/bioconda/linux-64/perl-xml-sax-expat-0.51-pl526_3.tar.bz2#dd0420867f8efc417116567491cccffa
https://conda.anaconda.org/bioconda/linux-64/perl-xml-twig-3.52-pl526_2.tar.bz2#3c3238fa183ea240a2a5b08a615dfd79
https://repo.anaconda.com/pkgs/main/linux-64/plotly-5.9.0-py37h06a4308_0.conda#0fa2708228c558c0d8725803ee811de8
https://conda.anaconda.org/bioconda/noarch/pymummer-0.11.0-pyhdfd78af_1.tar.bz2#6941d8dec72ed06363dc79005ffaab36
https://repo.anaconda.com/pkgs/main/linux-64/pyqt-5.9.2-py37h05f1152_2.conda#22e969c53ead5594414fdd72194df83b
https://conda.anaconda.org/bioconda/linux-64/pysam-0.15.3-py37hda2845c_1.tar.bz2#0ec5344c7be14a67a9c258f57150d43d
https://repo.anaconda.com/pkgs/main/noarch/python-dateutil-2.8.2-pyhd3eb1b0_0.conda#211ee00320b08a1ac9fea6677649f6c9
https://repo.anaconda.com/pkgs/main/linux-64/setuptools-65.6.3-py37h06a4308_0.conda#1039493adf22eff152d28326000c1f93
https://conda.anaconda.org/bioconda/linux-64/t_coffee-11.0.8-py37hea885bf_8.tar.bz2#eee20ab46d13f264a8957fed239d39b7
https://repo.anaconda.com/pkgs/main/linux-64/typing_extensions-4.4.0-py37h06a4308_0.conda#d7ab62b9397d8bae08cff8d8551984ef
https://conda.anaconda.org/bioconda/noarch/bio_assembly_refinement-0.5.1-py_2.tar.bz2#b7d00fded241f99f8c8be3e062c81fed
https://conda.anaconda.org/bioconda/linux-64/flye-2.8.1-py37h1c8e9b9_0.tar.bz2#a4196c823827b11b3e7848f8ba20a103
https://repo.anaconda.com/pkgs/main/linux-64/importlib-metadata-4.11.3-py37h06a4308_0.conda#805ade2a4aa932fcf4b598a4de33c2d0
https://repo.anaconda.com/pkgs/main/linux-64/kiwisolver-1.4.4-py37h6a678d5_0.conda#932b8e944691ebe2526744b84b985409
https://conda.anaconda.org/r/linux-64/numpy-base-1.17.0-py37hde5b4d6_0.tar.bz2#52ed8da767329ff715c2ff1967bb3971
https://repo.anaconda.com/pkgs/main/linux-64/pango-1.42.4-h049681c_0.conda#bfd8859e7ea05185e93cd73f9a1106b9
https://conda.anaconda.org/bioconda/linux-64/perl-class-load-0.25-pl526_0.tar.bz2#03c73103dc5e4f7daabd6bb0931193b6
https://conda.anaconda.org/bioconda/linux-64/perl-devel-overloadinfo-0.005-pl526_0.tar.bz2#c3f198e3bc81f5f1af1aedff4dbd9167
https://conda.anaconda.org/bioconda/linux-64/perl-http-message-6.18-pl526_0.tar.bz2#96eb00c7acca58e160fb34a41ea546c5
https://conda.anaconda.org/bioconda/linux-64/perl-image-info-1.38-pl526_1.tar.bz2#c317aa28d2ba5a73abb9a5d91ee7c988
https://conda.anaconda.org/bioconda/noarch/perl-net-http-6.19-pl526_0.tar.bz2#160f8e846ea37406d973acbf83b5a26b
https://conda.anaconda.org/bioconda/linux-64/perl-package-deprecationmanager-0.17-pl526_0.tar.bz2#b2f09a023ab3afe9f71a86776ee05e3b
https://conda.anaconda.org/bioconda/linux-64/perl-www-robotrules-6.02-pl526_3.tar.bz2#8b06331804b3b94eb99b3c1c4b7a4d72
https://conda.anaconda.org/bioconda/linux-64/perl-xml-libxslt-1.94-pl526_1.tar.bz2#d9e8421667819f405cba79dab4723bab
https://conda.anaconda.org/bioconda/linux-64/perl-xml-simple-2.25-pl526_1.tar.bz2#f410354a825d186da9f843f6ff9cd15e
https://conda.anaconda.org/bioconda/linux-64/samtools-1.9-h10a08f8_12.tar.bz2#a30f9567459497443fb98c5d46384769
https://conda.anaconda.org/bioconda/noarch/circlator-1.5.5-py_2.tar.bz2#93076e12d4889e077bb01271ddf3ecbf
https://repo.anaconda.com/pkgs/main/linux-64/graphviz-2.40.1-h21bd128_2.conda#54c61327f6e6f6e65ca20afc93ae35f5
https://repo.anaconda.com/pkgs/main/noarch/importlib_metadata-4.11.3-hd3eb1b0_0.conda#75a3ad10bde0ed37a345fc69ddf76475
https://conda.anaconda.org/r/linux-64/mkl_fft-1.0.14-py37hd81dba3_0.tar.bz2#b6a12e9c1da1c7ea67bec056eb9920ff
https://conda.anaconda.org/r/linux-64/mkl_random-1.0.4-py37hd81dba3_0.tar.bz2#5690976db67813140d53965cc56b3c75
https://conda.anaconda.org/bioconda/linux-64/perl-class-load-xs-0.10-pl526h6bb024c_2.tar.bz2#94e570466f327fdb7a83ed8e12523cfd
https://conda.anaconda.org/bioconda/linux-64/perl-data-stag-0.14-pl526_1.tar.bz2#3a50f48ef514466c9288b3151df08d8a
https://conda.anaconda.org/bioconda/linux-64/perl-http-cookies-6.04-pl526_0.tar.bz2#24c2429d0ac0467c11a34cae14f366ce
https://conda.anaconda.org/bioconda/linux-64/perl-http-daemon-6.01-pl526_1.tar.bz2#b6540672ea97f10b1088ece63b799177
https://conda.anaconda.org/bioconda/linux-64/perl-http-negotiate-6.01-pl526_3.tar.bz2#3be31b3d87352fdd54246212bae3ede9
https://conda.anaconda.org/bioconda/linux-64/perl-template-toolkit-2.26-pl526_1.tar.bz2#fa89ace236f54f558e7569b276338968
https://repo.anaconda.com/pkgs/main/noarch/argcomplete-1.12.3-pyhd3eb1b0_0.conda#fb4ef2f9a604f959e99741b902045bbf
https://conda.anaconda.org/r/linux-64/numpy-1.17.0-py37h7e9f1db_0.tar.bz2#0633e4ba4679b7f352484168b0ab182f
https://conda.anaconda.org/bioconda/noarch/perl-bio-phylo-0.58-pl5262hdfd78af_3.tar.bz2#5c1d7067424e815dbb5642dd2bd3eaf5
https://conda.anaconda.org/bioconda/linux-64/perl-graphviz-2.24-pl526h734ff71_0.tar.bz2#926d75742d73904e0f9b0eba0e2a11ec
https://conda.anaconda.org/bioconda/noarch/perl-libwww-perl-6.39-pl526_0.tar.bz2#54f96d7a0ea63cc4505f8cc653c831ee
https://conda.anaconda.org/bioconda/linux-64/perl-moose-2.2011-pl526hf484d3e_1.tar.bz2#3cbc780a48b996083b19cece0e7cdb2f
https://repo.anaconda.com/pkgs/main/linux-64/biopython-1.78-py37h7f8727e_0.conda#8934a3ac3aa9b1ddf38977de101f0276
https://repo.anaconda.com/pkgs/main/linux-64/h5py-3.7.0-py37h737f45e_0.conda#38526a0655e76d7449fd95920d448ffc
https://repo.anaconda.com/pkgs/main/linux-64/matplotlib-base-3.4.3-py37hbbc1b5f_0.conda#6505d447ef706816c5c9c3d49d497ba8
https://repo.anaconda.com/pkgs/main/linux-64/numba-0.54.1-py37h51133e4_0.conda#5ee7127ee44b2ca69be845acf16065cd
https://repo.anaconda.com/pkgs/main/linux-64/pandas-1.2.4-py37ha9443f7_0.conda#8dd9d486b5c1bb1357b2aa3338a6d87b
https://conda.anaconda.org/bioconda/linux-64/perl-lwp-protocol-https-6.07-pl526_4.tar.bz2#890387d167b855b7ba31853e8a470030
https://conda.anaconda.org/bioconda/linux-64/perl-moo-2.003004-pl526_0.tar.bz2#95008534c8c436981eb84793459fd532
https://conda.anaconda.org/bioconda/linux-64/perl-xml-dom-1.46-pl526_0.tar.bz2#0be82b3d737f4412d9a11481f5e74e8b
https://repo.anaconda.com/pkgs/main/linux-64/scipy-1.6.2-py37h91f5cce_0.conda#c10a9cbe368f7db402d2e0d0b9e4d135
https://repo.anaconda.com/pkgs/main/linux-64/matplotlib-3.4.3-py37h06a4308_0.conda#a41bd54f965eba7cb97307e4d836eb3f
https://conda.anaconda.org/bioconda/linux-64/perl-array-compare-3.0.1-pl526_1.tar.bz2#707a482cecc408d3574ac06c1d681211
https://conda.anaconda.org/bioconda/linux-64/perl-soap-lite-1.19-pl526_1.tar.bz2#5eff39fd516c8c8fbe1fe911150f38b2
https://conda.anaconda.org/bioconda/linux-64/perl-xml-dom-xpath-0.14-pl526_1.tar.bz2#c9bdd4aa6de4c1745ab959923beccb05
https://conda.anaconda.org/bioconda/noarch/pyfaidx-0.7.2.1-pyh7cba7a3_1.tar.bz2#71c5879674dee2e5e8c6e51e60d4acd6
https://repo.anaconda.com/pkgs/main/linux-64/scikit-learn-1.0.2-py37h51133e4_1.conda#d772c30017e91436c9fe85413b79613f
https://conda.anaconda.org/bioconda/noarch/gffutils-0.11.1-pyh7cba7a3_0.tar.bz2#ea7b36787ecdc57481398fe4d75d3076
https://conda.anaconda.org/bioconda/noarch/perl-bioperl-core-1.007002-pl5262hdfd78af_3.tar.bz2#1bef0cfcd0294e17aeea44bfc397f610
https://conda.anaconda.org/bioconda/noarch/panaroo-1.1.2-py_0.tar.bz2#cfc591b4538cd713b3aea81c1ea0fcbe
https://conda.anaconda.org/bioconda/noarch/perl-bio-asn1-entrezgene-1.73-pl5262hdfd78af_2.tar.bz2#ae612dabb9d0b59ac2287f6eefa12b40
https://conda.anaconda.org/bioconda/noarch/perl-bio-coordinate-1.007001-pl5262hdfd78af_2.tar.bz2#e1bf5881c8ac82e19c8d24861a1f9d19
https://conda.anaconda.org/bioconda/noarch/perl-bio-featureio-1.6.905-pl5262hdfd78af_3.tar.bz2#1d30df60376fa0c79768d9f85313f207
https://conda.anaconda.org/bioconda/linux-64/perl-bio-samtools-1.43-pl526h1341992_1.tar.bz2#477fdf7fd3dcfb7dc9b755f48d7c9175
https://conda.anaconda.org/bioconda/noarch/perl-bioperl-run-1.007002-pl5262hdfd78af_5.tar.bz2#bf6e302bd62eaf7a95f53136d9e71234
https://conda.anaconda.org/bioconda/noarch/perl-bio-tools-phylo-paml-1.7.3-pl5262hdfd78af_2.tar.bz2#c3a180cae8b54afc4fc7e0b130fde0df
https://conda.anaconda.org/bioconda/noarch/perl-bio-tools-run-alignment-clustalw-1.7.4-pl5262hdfd78af_2.tar.bz2#85f4d7898fc7911ff5f71c24c082075e
https://conda.anaconda.org/bioconda/noarch/perl-bio-tools-run-alignment-tcoffee-1.7.4-pl5262hdfd78af_3.tar.bz2#3a929bb2e5d30052660674d5c0f1d862
https://conda.anaconda.org/bioconda/noarch/perl-bioperl-1.7.2-pl526_11.tar.bz2#2fe21b69efb39401d28f27f398f7d26e
https://conda.anaconda.org/bioconda/linux-64/prokka-1.13-3.tar.bz2#048d50e78811ac9f152b5fd054587c68
assembly/container/environment.yml 0 → 100644
+ 23
− 0
View file @ dbda4ecc
name: pb_assembly
channels:
- bioconda
- r
- defaults
dependencies:
- flye
- samtools
- minimap2
- circlator
- prokka
- numpy
- scipy
- matplotlib
- scikit-learn
- pandas
- jinja2
- h5py
- pysam
- edlib
- python-edlib
- biopython
prefix: /home/cristobal/anaconda3/envs/pb_assembly
assembly/resources/H37Rv.gbf 0 → 100755
+ 0
− 0
View file @ dbda4ecc
Source diff could not be displayed: it is too large. Options to address this: view the blob.
assembly/samples.tsv 0 → 100755
+ 3
− 0
View file @ dbda4ecc
sample path
PB000180 /home/cristobal/TB/projects/pacbio_microscale/Figures/Fig2/c.duplication/m64156_230418_070808.bc2073--bc2073.hifi_reads.fastq.gz
\ No newline at end of file
assembly/workflow/Snakefile 0 → 100755
+ 34
− 0
View file @ dbda4ecc
containerized: "container/assemblySMK.sif"
include: "rules/common.smk"
include: "rules/readQC.smk"
include: "rules/assemble.smk"
include: "rules/circularize.smk"
include: "rules/annotate.smk"
include: "rules/summarize.smk"
if config["mapreads"] == "yes":
include: "rules/mapreads.smk"
rule all:
input:
"results/read_summaries.tsv",
"results/assembly_summaries.tsv",
expand("results/{sample}/prokka/{sample}.gff", sample = samples.keys()),
expand("results/{sample}/remapping/shortreads.bam", sample = samples.keys()),
expand("results/{sample}/remapping/longreads.bam", sample = samples.keys())
else:
rule all:
input:
"results/read_summaries.tsv",
"results/assembly_summaries.tsv",
expand("results/{sample}/prokka/{sample}.gff", sample = samples.keys())
assembly/workflow/rules/annotate.smk 0 → 100755
+ 27
− 0
View file @ dbda4ecc
rule prokka:
input: "results/{sample}/assembly.circularized.renamed.fasta"
output: "results/{sample}/prokka/{sample}.gff"
params:
refgbf = config["ref"]["gbf"],
asm = "{sample}",
outdir = "results/{sample}/prokka"
threads: config["threads"]
envmodules: "prokka/1.14.5-gompi-2021a"
shell:
"""
prokka {input} \
--force \
--kingdom Bacteria \
--genus Mycobacterium \
--species tuberculosis \
--strain {params.asm} \
--addgenes \
--proteins {params.refgbf} \
--prefix {params.asm} \
--locustag {params.asm} \
--cpus {threads} \
--outdir {params.outdir}
"""
assembly/workflow/rules/assemble.smk 0 → 100755
+ 18
− 0
View file @ dbda4ecc
rule flye:
input: lambda wildcards: samples[wildcards.sample].longread_fastq
output: "results/{sample}/assembly.fasta", "results/{sample}/assembly_info.txt"
threads: config["threads"]
params:
genome_size = config["ref"]["genome_size"],
outdir = "results/{sample}"
shell:
"""
flye \
--pacbio-hifi {input} \
--genome-size {params.genome_size} \
--threads {threads} \
--out-dir {params.outdir}
"""
assembly/workflow/rules/circularize.smk 0 → 100755
+ 108
− 0
View file @ dbda4ecc
rule mapreads:
input:
assembly = 'results/{sample}/assembly.fasta',
reads = lambda wildcards: expand(samples[wildcards.sample].longread_fastq)
output: "results/{sample}/circlator/01.mapreads.bam"
params:
threads = config["threads"]
shell:
"""
circlator mapreads {input.assembly} {input.reads} {output} --threads {params.threads}
"""
rule bam2reads:
input: "results/{sample}/circlator/01.mapreads.bam"
output: "results/{sample}/circlator/02.bam2reads.fasta"
params:
output_pref = "results/{sample}/circlator/02.bam2reads"
shell:
"""
circlator bam2reads {input} {params.output_pref} --discard_unmapped
"""
rule localassembly:
input: "results/{sample}/circlator/02.bam2reads.fasta"
output: "results/{sample}/circlator/03.assemble/assembly.fasta"
params:
outdir = "results/{sample}/circlator/03.assemble",
threads = config["threads"]
shell:
"""
flye --pacbio-hifi {input} --out-dir {params.outdir} --genome-size 100k --threads {params.threads}
"""
rule merge:
input:
assembly = 'results/{sample}/assembly.fasta',
localassembly = "results/{sample}/circlator/03.assemble/assembly.fasta"
output: "results/{sample}/circlator/04.merge.fasta"
params:
threads = config["threads"],
output_pref = "results/{sample}/circlator/04.merge"
shell:
"""
circlator merge {input.assembly} {input.localassembly} {params.output_pref} --threads {params.threads}
"""
rule clean:
input: "results/{sample}/circlator/04.merge.fasta"
output: "results/{sample}/circlator/05.clean.fasta"
params:
output_pref = "results/{sample}/circlator/05.clean"
shell:
"""
circlator clean {input} {params.output_pref}
"""
rule fixstart:
input: "results/{sample}/circlator/05.clean.fasta"
output: "results/{sample}/circlator/06.fixstart.fasta"
params:
output_pref = "results/{sample}/circlator/06.fixstart"
shell:
"""
circlator fixstart {input} {params.output_pref}
"""
rule rename:
input:
assembly = "results/{sample}/circlator/06.fixstart.fasta"
params:
prefix = "{sample}",
keep_intermediate = config["keep_intermediate"]
output: "results/{sample}/assembly.circularized.renamed.fasta"
run:
import os
import sys
from Bio import SeqIO
contig_NR = 1
fasta_handle = open(output[0], "w")
with open(input.assembly) as original:
records = SeqIO.parse(original, 'fasta')
for record in records:
record.id = params.prefix + "_" + str(contig_NR)
record.description = ""
SeqIO.write(record, fasta_handle, 'fasta')
contig_NR += 1
fasta_handle.close()
assembly/workflow/rules/cleanup.smk 0 → 100644
+ 8
− 0
View file @ dbda4ecc
# Remove circlator and pilon intermediate results, which take up a lot of space
if [ {params.keep_intermediate} == "No" ]; then
rm results/{params.prefix}/noduplicates.fastq.gz
rm -r results/{params.prefix}/pilon
rm -r results/{params.prefix}/circlator
fi
\ No newline at end of file
assembly/workflow/rules/common.smk 0 → 100755
+ 14
− 0
View file @ dbda4ecc
configfile: "config.yaml"
class sample:
def __init__(self, fields):
self.id = fields[0]
self.longread_fastq = fields[1]
samples = {}
with open(config["samples"]) as f:
next(f)
for line in f:
fields = line.strip().split("\t")
samples[fields[0]] = sample(fields)
assembly/workflow/rules/mapreads.smk 0 → 100644
+ 35
− 0
View file @ dbda4ecc
rule map_SR:
input:
reads = lambda wildcards: samples[wildcards.sample].shortread_fastq,
assembly = "results/{sample}/assembly.circularized.renamed.fasta"
output: "results/{sample}/remapping/shortreads.bam"
params:
intermediate = "results/{sample}/remapping/shortreads.raw.bam"
threads: config["threads"]
shell:
"""
minimap2 -ax sr {input.assembly} {input.reads} | samtools view -hu > {params.intermediate}
samtools sort -@ {threads} {params.intermediate} -o {output}
samtools index {output}
rm {params.intermediate}
"""
rule map_LR:
input:
reads = lambda wildcards: samples[wildcards.sample].longread_fastq,
assembly = "results/{sample}/assembly.circularized.renamed.fasta"
output: "results/{sample}/remapping/longreads.bam"
params:
intermediate = "results/{sample}/remapping/longreads.raw.bam"
threads: config["threads"]
shell:
"""
minimap2 -ax map-hifi {input.assembly} {input.reads} | samtools view -hu > {params.intermediate}
samtools sort -@ {threads} {params.intermediate} -o {output}
samtools index {output}
rm {params.intermediate}
"""
\ No newline at end of file
assembly/workflow/rules/readQC.smk 0 → 100755
+ 14
− 0
View file @ dbda4ecc
rule longQC:
input: lambda wildcards: samples[wildcards.sample].longread_fastq
output: "results/{sample}/longqc/QC_vals_longQC_sampleqc.json"
params:
threads = config["threads"],
outfolder = "results/{sample}/longqc/"
shell:
"""
rm -r {params.outfolder}
python /LongQC/longQC.py sampleqc -x pb-sequel -o {params.outfolder}/ -p {params.threads} {input}
"""
assembly/workflow/rules/summarize.smk 0 → 100644
+ 83
− 0
View file @ dbda4ecc
rule read_summary:
input: expand("results/{sample}/longqc/QC_vals_longQC_sampleqc.json", sample = samples.keys())
output: "results/read_summaries.tsv"
run:
import json
sample_d = {}
header = ["sample"]
for FILE in input:
sample = FILE.split("/")[1]
d = json.load(open(FILE))
d_flat = {}
for a_id, a_info in d.items():
if isinstance(a_info, dict):
for b_id, b_info in a_info.items():
if b_id == "gamma_params":
continue
d_flat[b_id] = b_info
if b_id not in header:
header.append(b_id)
else:
d_flat[a_id] = a_info
if a_id not in header:
header.append(a_id)
sample_d[sample] = d_flat
with open(output[0], "w") as f:
f.write('\t'.join(header) + '\n')
for sample in sample_d:
outline = [sample]
for k in header[1:]:
if k in sample_d[sample]:
outline.append(str(sample_d[sample][k]))
else:
outline.append("NA")
f.write('\t'.join(outline) + '\n')
rule assembly_summaries:
input: expand("results/{sample}/assembly_info.txt", sample = samples.keys())
output: "results/assembly_summaries.tsv"
run:
header = ""
outfile = open(output[0], "w")
outfile_single_contigs = open("results/single_contig_samples.txt", "w")
for FILE in input:
sample = FILE.split("/")[1]
contig_count = 0
with open(FILE) as f:
if not header:
header = "sample\t" + next(f)
outfile.write(header)
else:
next(f)
for line in f:
outline = sample + "\t" + line
outfile.write(outline)
contig_count += 1
if contig_count == 1:
outfile_single_contigs.write(sample + '\n')
outfile.close()
fig.png 0 → 100644
+ 0
− 0
View file @ dbda4ecc
fig.png

41.8 KiB

0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Please register or to comment