add modularized workflow with kraken2 for contamination removal to new branch for testing
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- .gitignore 3 additions, 5 deletions.gitignore
- .gitmodules 6 additions, 6 deletions.gitmodules
- README.md 105 additions, 119 deletionsREADME.md
- Snakefile 95 additions, 0 deletionsSnakefile
- example_data/altref/chr21_remap.fa 766375 additions, 0 deletionsexample_data/altref/chr21_remap.fa
- example_data/altref/chr21_remap.fa.amb 40 additions, 0 deletionsexample_data/altref/chr21_remap.fa.amb
- example_data/altref/chr21_remap.fa.ann 3 additions, 0 deletionsexample_data/altref/chr21_remap.fa.ann
- example_data/altref/chr21_remap.fa.bwt 0 additions, 0 deletionsexample_data/altref/chr21_remap.fa.bwt
- example_data/altref/chr21_remap.fa.pac 0 additions, 0 deletionsexample_data/altref/chr21_remap.fa.pac
- example_data/altref/chr21_remap.fa.sa 0 additions, 0 deletionsexample_data/altref/chr21_remap.fa.sa
- example_data/ref/chr21_ins.fa 0 additions, 0 deletionsexample_data/ref/chr21_ins.fa
- example_data/ref/chr21_ins.fa.amb 40 additions, 0 deletionsexample_data/ref/chr21_ins.fa.amb
- example_data/ref/chr21_ins.fa.ann 3 additions, 0 deletionsexample_data/ref/chr21_ins.fa.ann
- example_data/ref/chr21_ins.fa.bwt 0 additions, 0 deletionsexample_data/ref/chr21_ins.fa.bwt
- example_data/ref/chr21_ins.fa.fai 1 addition, 0 deletionsexample_data/ref/chr21_ins.fa.fai
- example_data/ref/chr21_ins.fa.pac 0 additions, 0 deletionsexample_data/ref/chr21_ins.fa.pac
- example_data/ref/chr21_ins.fa.sa 0 additions, 0 deletionsexample_data/ref/chr21_ins.fa.sa
- example_data/virus_ref/altref_virus_clean.fa 0 additions, 0 deletionsexample_data/virus_ref/altref_virus_clean.fa
- example_data/virus_ref/altref_virus_clean.fa.amb 0 additions, 9891 deletionsexample_data/virus_ref/altref_virus_clean.fa.amb
- example_data/virus_ref/altref_virus_clean.fa.ann 0 additions, 29863 deletionsexample_data/virus_ref/altref_virus_clean.fa.ann
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