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- .gitignore 2 additions, 0 deletions.gitignore
- README.md 20 additions, 0 deletionsREADME.md
- assembly/README.md 77 additions, 0 deletionsassembly/README.md
- assembly/config.yaml 18 additions, 0 deletionsassembly/config.yaml
- assembly/container/README.md 49 additions, 0 deletionsassembly/container/README.md
- assembly/container/assemblySC.def 54 additions, 0 deletionsassembly/container/assemblySC.def
- assembly/container/conda-linux-64.lock 0 additions, 0 deletionsassembly/container/conda-linux-64.lock
- assembly/container/environment.yml 23 additions, 0 deletionsassembly/container/environment.yml
- assembly/resources/H37Rv.gbf 0 additions, 0 deletionsassembly/resources/H37Rv.gbf
- assembly/samples.tsv 3 additions, 0 deletionsassembly/samples.tsv
- assembly/workflow/Snakefile 34 additions, 0 deletionsassembly/workflow/Snakefile
- assembly/workflow/rules/annotate.smk 27 additions, 0 deletionsassembly/workflow/rules/annotate.smk
- assembly/workflow/rules/assemble.smk 18 additions, 0 deletionsassembly/workflow/rules/assemble.smk
- assembly/workflow/rules/circularize.smk 108 additions, 0 deletionsassembly/workflow/rules/circularize.smk
- assembly/workflow/rules/cleanup.smk 8 additions, 0 deletionsassembly/workflow/rules/cleanup.smk
- assembly/workflow/rules/common.smk 14 additions, 0 deletionsassembly/workflow/rules/common.smk
- assembly/workflow/rules/mapreads.smk 35 additions, 0 deletionsassembly/workflow/rules/mapreads.smk
- assembly/workflow/rules/readQC.smk 14 additions, 0 deletionsassembly/workflow/rules/readQC.smk
- assembly/workflow/rules/summarize.smk 83 additions, 0 deletionsassembly/workflow/rules/summarize.smk
- fig.png 0 additions, 0 deletionsfig.png
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