README.md
setup.py
itm_helper/__init__.py
itm_helper/alpha_diversity.py
itm_helper/beta_diversity.py
itm_helper/combine_bracken_outputs.py
itm_helper/combine_kreports.py
itm_helper/combine_mpa.py
itm_helper/extract_kraken_reads.py
itm_helper/kraken2otu.py
itm_helper/kreport2krona.py
itm_helper/kreport2mpa.py
itm_helper/make_kreport.py
itm_helper/make_ktaxonomy.py
itmfinder.egg-info/PKG-INFO
itmfinder.egg-info/SOURCES.txt
itmfinder.egg-info/dependency_links.txt
itmfinder.egg-info/entry_points.txt
itmfinder.egg-info/requires.txt
itmfinder.egg-info/top_level.txt
utils/__init__.py
utils/data_loader.py
workflow/__init__.py
workflow/step1_fastq_qc.py
workflow/step2_remove_host_reads.py
workflow/step2_remove_host_reads2.py
workflow/step3_kraken2.py
workflow/step4_extract_microbiome_reads.py
workflow/step5_decontamination.py
workflow/step6_kraken2Bracken.py
workflow/step7_merge_itm_results.py
workflow/step8_get_data_summary.py