├── .gitignore ├── README.md ├── data ├── p33_aka_abc33_species_list.txt └── p33_sra │ └── README ├── pylintrc ├── src ├── S16.py ├── S16_prefilter.py ├── classify_hits.py ├── convert_table.py ├── ident_to_bam.py ├── plot_rarefaction.py ├── primer_trimmer.py ├── primer_trimmer.py.README └── snake.make └── test_all.sh /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/GERMS_16S_pipeline/HEAD/.gitignore -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/GERMS_16S_pipeline/HEAD/README.md -------------------------------------------------------------------------------- /data/p33_aka_abc33_species_list.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/GERMS_16S_pipeline/HEAD/data/p33_aka_abc33_species_list.txt -------------------------------------------------------------------------------- /data/p33_sra/README: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/GERMS_16S_pipeline/HEAD/data/p33_sra/README -------------------------------------------------------------------------------- /pylintrc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/GERMS_16S_pipeline/HEAD/pylintrc -------------------------------------------------------------------------------- /src/S16.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/GERMS_16S_pipeline/HEAD/src/S16.py -------------------------------------------------------------------------------- /src/S16_prefilter.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/GERMS_16S_pipeline/HEAD/src/S16_prefilter.py -------------------------------------------------------------------------------- /src/classify_hits.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/GERMS_16S_pipeline/HEAD/src/classify_hits.py -------------------------------------------------------------------------------- /src/convert_table.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/GERMS_16S_pipeline/HEAD/src/convert_table.py -------------------------------------------------------------------------------- /src/ident_to_bam.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/GERMS_16S_pipeline/HEAD/src/ident_to_bam.py -------------------------------------------------------------------------------- /src/plot_rarefaction.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/GERMS_16S_pipeline/HEAD/src/plot_rarefaction.py -------------------------------------------------------------------------------- /src/primer_trimmer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/GERMS_16S_pipeline/HEAD/src/primer_trimmer.py -------------------------------------------------------------------------------- /src/primer_trimmer.py.README: -------------------------------------------------------------------------------- 1 | Taken from original 16S pipeline on 2015-08-15 2 | -------------------------------------------------------------------------------- /src/snake.make: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/GERMS_16S_pipeline/HEAD/src/snake.make -------------------------------------------------------------------------------- /test_all.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CSB5/GERMS_16S_pipeline/HEAD/test_all.sh --------------------------------------------------------------------------------