Read Sequencer
Overview
Read Sequencer is a python package to simulate sequencing. It reads fasta files, simulate sequencing with specified read length and writes the resulting sequences into a new fasta file.
Installation from github
Read Sequencer requires Python 3.9 or later.
Install Read Sequencer from Github using:
git clone https://git.scicore.unibas.ch/zavolan_group/tools/read-sequencer.git
cd read-sequencer
pip install . Usage
usage: readsequencer [-h] [-i INPUT] [-r READ_LENGTH] [-n N_RANDOM] [-s CHUNK_SIZE] output
Simulates sequencing of DNA sequences specified by an FASTA file.
positional arguments:
output path to FASTA file
optional arguments:
-h, --help show this help message and exit
-i INPUT, --input INPUT
path to FASTA file
-r READ_LENGTH, --read-length READ_LENGTH
read length for sequencing
-n N_RANDOM, --n_random N_RANDOM
n random sequences. Just used if input fasta file is not specified.
-s CHUNK_SIZE, --chunk-size CHUNK_SIZE
chunk_size for batch processing
Docker
The docker image is available on docker hub: https://hub.docker.com/r/grrchrr/readsequencer
docker pull grrchrr/readsequencer
docker run readsequencer --helpContributors and Contact Information
Christoph Harmel - christoph.harmel@unibas.ch
Michael Sandholzer - michael.sandholzer@unibas.ch
Clara Serger - c.serger@unibas.ch