LICENSE
MANIFEST.in
README.md
setup.py
hecatomb/__init__.py
hecatomb/__main__.py
hecatomb/hecatomb.CITATION
hecatomb/hecatomb.LICENSE
hecatomb/hecatomb.VERSION
hecatomb.egg-info/PKG-INFO
hecatomb.egg-info/SOURCES.txt
hecatomb.egg-info/dependency_links.txt
hecatomb.egg-info/entry_points.txt
hecatomb.egg-info/requires.txt
hecatomb.egg-info/top_level.txt
hecatomb/snakemake/config/config.yaml
hecatomb/snakemake/config/dbFiles.yaml
hecatomb/snakemake/config/immutable.yaml
hecatomb/snakemake/profile/default/config.yaml
hecatomb/snakemake/profile/example_slurm/config.yaml
hecatomb/snakemake/profile/example_slurm/slurm-status.py
hecatomb/snakemake/workflow/AddHost.smk
hecatomb/snakemake/workflow/DownloadDB.smk
hecatomb/snakemake/workflow/Hecatomb.smk
hecatomb/snakemake/workflow/combineOutputs.smk
hecatomb/snakemake/workflow/container/bbmap
hecatomb/snakemake/workflow/container/bedtools
hecatomb/snakemake/workflow/container/canu
hecatomb/snakemake/workflow/container/curl
hecatomb/snakemake/workflow/container/koverage
hecatomb/snakemake/workflow/container/krona
hecatomb/snakemake/workflow/container/megahit
hecatomb/snakemake/workflow/container/metaflye
hecatomb/snakemake/workflow/container/minimap2
hecatomb/snakemake/workflow/container/mmseqs2
hecatomb/snakemake/workflow/container/pigz
hecatomb/snakemake/workflow/container/pysam
hecatomb/snakemake/workflow/container/samtools
hecatomb/snakemake/workflow/container/seqkit
hecatomb/snakemake/workflow/container/trimnami
hecatomb/snakemake/workflow/envs/bbmap.yaml
hecatomb/snakemake/workflow/envs/bedtools.yaml
hecatomb/snakemake/workflow/envs/canu.yaml
hecatomb/snakemake/workflow/envs/curl.yaml
hecatomb/snakemake/workflow/envs/koverage.yaml
hecatomb/snakemake/workflow/envs/krona.yaml
hecatomb/snakemake/workflow/envs/megahit.yaml
hecatomb/snakemake/workflow/envs/metaflye.yaml
hecatomb/snakemake/workflow/envs/minimap2.yaml
hecatomb/snakemake/workflow/envs/mmseqs2.yaml
hecatomb/snakemake/workflow/envs/pigz.yaml
hecatomb/snakemake/workflow/envs/pysam.yaml
hecatomb/snakemake/workflow/envs/samtools.yaml
hecatomb/snakemake/workflow/envs/seqkit.yaml
hecatomb/snakemake/workflow/envs/trimnami.yaml
hecatomb/snakemake/workflow/report/host_removed_counts.rst
hecatomb/snakemake/workflow/report/mapped_counts.rst
hecatomb/snakemake/workflow/report/nucleotide_annotations.rst
hecatomb/snakemake/workflow/report/protein_annotations.rst
hecatomb/snakemake/workflow/report/raw_read_counts.rst
hecatomb/snakemake/workflow/report/sankey.rst
hecatomb/snakemake/workflow/report/step07.rst
hecatomb/snakemake/workflow/report/step08.rst
hecatomb/snakemake/workflow/report/step09.rst
hecatomb/snakemake/workflow/report/step10.rst
hecatomb/snakemake/workflow/report/step11.rst
hecatomb/snakemake/workflow/report/step12.rst
hecatomb/snakemake/workflow/report/step13.rst
hecatomb/snakemake/workflow/report/summary_table.rst
hecatomb/snakemake/workflow/report/tax_level_counts.rst
hecatomb/snakemake/workflow/report/unclassified_seqtable.rst
hecatomb/snakemake/workflow/rules/annotation/contig_annotation.smk
hecatomb/snakemake/workflow/rules/annotation/contig_mapping.smk
hecatomb/snakemake/workflow/rules/annotation/read_annotation.smk
hecatomb/snakemake/workflow/rules/assembly/coverage.smk
hecatomb/snakemake/workflow/rules/assembly/longreads.smk
hecatomb/snakemake/workflow/rules/assembly/shortreads.smk
hecatomb/snakemake/workflow/rules/preflight/directories.smk
hecatomb/snakemake/workflow/rules/preflight/functions.smk
hecatomb/snakemake/workflow/rules/preflight/targets.smk
hecatomb/snakemake/workflow/rules/preflight/validate.smk
hecatomb/snakemake/workflow/rules/preprocessing/preprocessing.smk
hecatomb/snakemake/workflow/rules/reports/summaries.smk
hecatomb/snakemake/workflow/rules/reports/summaries_optional.smk
hecatomb/snakemake/workflow/scripts/__init__.py
hecatomb/snakemake/workflow/scripts/aaBigtable.py
hecatomb/snakemake/workflow/scripts/aaPrimaryParse.py
hecatomb/snakemake/workflow/scripts/aaSecondaryParse.py
hecatomb/snakemake/workflow/scripts/contigCountTable.py
hecatomb/snakemake/workflow/scripts/contigKronaText.py
hecatomb/snakemake/workflow/scripts/contigReadTaxon.py
hecatomb/snakemake/workflow/scripts/kronaText.py
hecatomb/snakemake/workflow/scripts/mergeSeqTable.py
hecatomb/snakemake/workflow/scripts/ntBigtable.py
hecatomb/snakemake/workflow/scripts/ntPrimaryParse.py
hecatomb/snakemake/workflow/scripts/ntSecondaryLca.py
hecatomb/snakemake/workflow/scripts/orfmFilt.py
hecatomb/snakemake/workflow/scripts/sankey.py
hecatomb/snakemake/workflow/scripts/seqPropertyTable.py
hecatomb/snakemake/workflow/scripts/taxLevelCounts.py
hecatomb/test_data/A13-04-182-06_TAGCTT_R1.fastq.gz
hecatomb/test_data/A13-04-182-06_TAGCTT_R2.fastq.gz
hecatomb/test_data/A13-12-250-06_GGCTAC_R1.fastq.gz
hecatomb/test_data/A13-12-250-06_GGCTAC_R2.fastq.gz
hecatomb/test_data/A13-135-177-06_AGTTCC_R1.fastq.gz
hecatomb/test_data/A13-135-177-06_AGTTCC_R2.fastq.gz
hecatomb/test_data/A13-151-169-06_ATGTCA_R1.fastq.gz
hecatomb/test_data/A13-151-169-06_ATGTCA_R2.fastq.gz
hecatomb/test_data/A13-252-114-06_CCGTCC_R1.fastq.gz
hecatomb/test_data/A13-252-114-06_CCGTCC_R2.fastq.gz
hecatomb/test_data/A13-253-140-06_GTCCGC_R1.fastq.gz
hecatomb/test_data/A13-253-140-06_GTCCGC_R2.fastq.gz
hecatomb/test_data/A13-255-183-06_GTGGCC_R1.fastq.gz
hecatomb/test_data/A13-255-183-06_GTGGCC_R2.fastq.gz
hecatomb/test_data/A13-256-115-06_GTTTCG_R1.fastq.gz
hecatomb/test_data/A13-256-115-06_GTTTCG_R2.fastq.gz
hecatomb/test_data/A13-256-117-06_ACTGAT_R1.fastq.gz
hecatomb/test_data/A13-256-117-06_ACTGAT_R2.fastq.gz
hecatomb/test_data/A13-258-124-06_CGTACG_R1.fastq.gz
hecatomb/test_data/A13-258-124-06_CGTACG_R2.fastq.gz
hecatomb/test_data/test_config.yaml
tests/test_hecatomb.py