python-scripts/ecolityper
site-packages/ecoliTyper/__init__.py
site-packages/ecoliTyper/core/__init__.py
site-packages/ecoliTyper/core/banner.py
site-packages/ecoliTyper/ecolityper.py
site-packages/ecoliTyper/modules/Abricate_module/ecoli_abricate.py
site-packages/ecoliTyper/modules/Amrfinder_module/bin/amr_report
site-packages/ecoliTyper/modules/Amrfinder_module/bin/amrfinder
site-packages/ecoliTyper/modules/Amrfinder_module/bin/amrfinder_index
site-packages/ecoliTyper/modules/Amrfinder_module/bin/amrfinder_update
site-packages/ecoliTyper/modules/Amrfinder_module/bin/disruption2genesymbol
site-packages/ecoliTyper/modules/Amrfinder_module/bin/dna_mutation
site-packages/ecoliTyper/modules/Amrfinder_module/bin/fasta2parts
site-packages/ecoliTyper/modules/Amrfinder_module/bin/fasta_check
site-packages/ecoliTyper/modules/Amrfinder_module/bin/fasta_extract
site-packages/ecoliTyper/modules/Amrfinder_module/bin/gff_check
site-packages/ecoliTyper/modules/Amrfinder_module/bin/mutate
site-packages/ecoliTyper/modules/Amrfinder_module/bin/stx/fasta_check
site-packages/ecoliTyper/modules/Amrfinder_module/bin/stx/fasta_extract
site-packages/ecoliTyper/modules/Amrfinder_module/bin/stx/stx.prot
site-packages/ecoliTyper/modules/Amrfinder_module/bin/stx/stxtyper
site-packages/ecoliTyper/modules/Amrfinder_module/bin/stx/test/amrfinder_integration.expected
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site-packages/ecoliTyper/modules/Amrfinder_module/bin/stx/test/amrfinder_integration2.fa
site-packages/ecoliTyper/modules/Amrfinder_module/bin/stx/test/basic.expected
site-packages/ecoliTyper/modules/Amrfinder_module/bin/stx/test/basic.fa
site-packages/ecoliTyper/modules/Amrfinder_module/bin/stx/test/basic.nuc_out.expected
site-packages/ecoliTyper/modules/Amrfinder_module/bin/stx/test/cases.expected
site-packages/ecoliTyper/modules/Amrfinder_module/bin/stx/test/cases.fa
site-packages/ecoliTyper/modules/Amrfinder_module/bin/stx/test/synthetics.expected
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site-packages/ecoliTyper/modules/Amrfinder_module/bin/stx/test/virulence_ecoli.expected
site-packages/ecoliTyper/modules/Amrfinder_module/bin/stx/test/virulence_ecoli.fa
site-packages/ecoliTyper/modules/Amrfinder_module/bin/stx/test_stxtyper.sh
site-packages/ecoliTyper/modules/Amrfinder_module/bin/stx/version.txt
site-packages/ecoliTyper/modules/Amrfinder_module/bin/stxtyper
site-packages/ecoliTyper/modules/Amrfinder_module/bin/test_amrfinder.sh
site-packages/ecoliTyper/modules/Amrfinder_module/bin/test_both.expected
site-packages/ecoliTyper/modules/Amrfinder_module/bin/test_disrupt.expected
site-packages/ecoliTyper/modules/Amrfinder_module/bin/test_disrupt.fa
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site-packages/ecoliTyper/modules/Amrfinder_module/bin/version.txt
site-packages/ecoliTyper/modules/Amrfinder_module/database.sh
site-packages/ecoliTyper/modules/Amrfinder_module/ecoli_amrfinder.py
site-packages/ecoliTyper/modules/CHTyper_module/CHTyper-fixed.py
site-packages/ecoliTyper/modules/CHTyper_module/blaster.py
site-packages/ecoliTyper/modules/CHTyper_module/chtyper_db/config
site-packages/ecoliTyper/modules/CHTyper_module/chtyper_db/fimH.fsa
site-packages/ecoliTyper/modules/CHTyper_module/chtyper_db/fumC.fsa
site-packages/ecoliTyper/modules/CHTyper_module/enhanced_chtyper.py
site-packages/ecoliTyper/modules/Ecoli_lineage/ecoli_comprehensive_reference.html
site-packages/ecoliTyper/modules/Ecoli_lineage/ecoli_html_reference.py
site-packages/ecoliTyper/modules/Ecoli_lineage/ecoli_lineage_database.py
site-packages/ecoliTyper/modules/Summary_module/genius_reporter.py
site-packages/ecoliTyper/modules/Visualization_module/visualization_reporter.py
site-packages/ecoliTyper/modules/fasta_qc_module/ecolityper_fasta_qc.py
site-packages/ecoliTyper/modules/mlst_module/bin/mlst
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site-packages/ecoliTyper/modules/mlst_module/db/scheme_species_map.tab
site-packages/ecoliTyper/modules/mlst_module/ecolimlst_module.py
site-packages/ecoliTyper/modules/mlst_module/perl5/MLST/Logger.pm
site-packages/ecoliTyper/modules/mlst_module/perl5/MLST/PubMLST.pm
site-packages/ecoliTyper/modules/mlst_module/perl5/MLST/Requirements.pm
site-packages/ecoliTyper/modules/mlst_module/perl5/MLST/Scheme.pm
site-packages/ecoliTyper/modules/mlst_module/perl5/Path/Tiny.pm
site-packages/ecoliTyper/modules/mlst_module/scripts/mlst-make_blast_db
site-packages/ecoliTyper/modules/mlst_module/scripts/mlst-show_seqs
site-packages/ecoliTyper/modules/phylogrouping_module/enhanced_ezclermont.py
site-packages/ecoliTyper/modules/serotypefinder_module/enhanced_serotypefinder.py
site-packages/ecoliTyper/modules/serotypefinder_module/serotypefinder.py
site-packages/ecoliTyper/modules/serotypefinder_module/serotypefinder_db/H_type.comp.b
site-packages/ecoliTyper/modules/serotypefinder_module/serotypefinder_db/H_type.fsa
site-packages/ecoliTyper/modules/serotypefinder_module/serotypefinder_db/H_type.length.b
site-packages/ecoliTyper/modules/serotypefinder_module/serotypefinder_db/H_type.name
site-packages/ecoliTyper/modules/serotypefinder_module/serotypefinder_db/H_type.seq.b
site-packages/ecoliTyper/modules/serotypefinder_module/serotypefinder_db/INSTALL.py
site-packages/ecoliTyper/modules/serotypefinder_module/serotypefinder_db/O_type.comp.b
site-packages/ecoliTyper/modules/serotypefinder_module/serotypefinder_db/O_type.fsa
site-packages/ecoliTyper/modules/serotypefinder_module/serotypefinder_db/O_type.length.b
site-packages/ecoliTyper/modules/serotypefinder_module/serotypefinder_db/O_type.name
site-packages/ecoliTyper/modules/serotypefinder_module/serotypefinder_db/O_type.seq.b
site-packages/ecoliTyper/modules/serotypefinder_module/serotypefinder_db/VERSION
site-packages/ecoliTyper/modules/serotypefinder_module/serotypefinder_db/config
site-packages/ecoliTyper/modules/serotypefinder_module/serotypefinder_db/kma/.github/workflows/linux-manual.yml
site-packages/ecoliTyper/modules/serotypefinder_module/serotypefinder_db/kma/.github/workflows/noarch-manual.yml
site-packages/ecoliTyper/modules/serotypefinder_module/serotypefinder_db/kma/.github/workflows/osx-manual.yml
site-packages/ecoliTyper/modules/serotypefinder_module/serotypefinder_db/kma/.github/workflows/release.yml
site-packages/ecoliTyper/modules/serotypefinder_module/serotypefinder_db/kma/KMAspecification.pdf
site-packages/ecoliTyper/modules/serotypefinder_module/serotypefinder_db/kma/Makefile
site-packages/ecoliTyper/modules/serotypefinder_module/serotypefinder_db/kma/README.md
site-packages/ecoliTyper/modules/serotypefinder_module/serotypefinder_db/kma/align.c
site-packages/ecoliTyper/modules/serotypefinder_module/serotypefinder_db/kma/align.h
site-packages/ecoliTyper/modules/serotypefinder_module/serotypefinder_db/kma/align.o
site-packages/ecoliTyper/modules/serotypefinder_module/serotypefinder_db/kma/alnfrags.c
site-packages/ecoliTyper/modules/serotypefinder_module/serotypefinder_db/kma/alnfrags.h
site-packages/ecoliTyper/modules/serotypefinder_module/serotypefinder_db/kma/alnfrags.o
site-packages/ecoliTyper/modules/serotypefinder_module/serotypefinder_db/kma/ankers.c
site-packages/ecoliTyper/modules/serotypefinder_module/serotypefinder_db/kma/ankers.h
site-packages/ecoliTyper/modules/serotypefinder_module/serotypefinder_db/kma/ankers.o
site-packages/ecoliTyper/modules/serotypefinder_module/serotypefinder_db/kma/assembly.c
site-packages/ecoliTyper/modules/serotypefinder_module/serotypefinder_db/kma/assembly.h
site-packages/ecoliTyper/modules/serotypefinder_module/serotypefinder_db/kma/assembly.o
site-packages/ecoliTyper/modules/serotypefinder_module/serotypefinder_db/kma/bitbucket-pipelines.yml
site-packages/ecoliTyper/modules/serotypefinder_module/serotypefinder_db/kma/chain.c
site-packages/ecoliTyper/modules/serotypefinder_module/serotypefinder_db/kma/chain.h
site-packages/ecoliTyper/modules/serotypefinder_module/serotypefinder_db/kma/chain.o
site-packages/ecoliTyper/modules/serotypefinder_module/serotypefinder_db/kma/cmp.c
site-packages/ecoliTyper/modules/serotypefinder_module/serotypefinder_db/kma/cmp.h
site-packages/ecoliTyper/modules/serotypefinder_module/serotypefinder_db/kma/cmp.o
site-packages/ecoliTyper/modules/serotypefinder_module/serotypefinder_db/kma/compdna.c
site-packages/ecoliTyper/modules/serotypefinder_module/serotypefinder_db/kma/compdna.h
site-packages/ecoliTyper/modules/serotypefinder_module/serotypefinder_db/kma/compdna.o
site-packages/ecoliTyper/modules/serotypefinder_module/serotypefinder_db/kma/compkmers.c
site-packages/ecoliTyper/modules/serotypefinder_module/serotypefinder_db/kma/compkmers.h
site-packages/ecoliTyper/modules/serotypefinder_module/serotypefinder_db/kma/compkmers.o
site-packages/ecoliTyper/modules/serotypefinder_module/serotypefinder_db/kma/compress.c
site-packages/ecoliTyper/modules/serotypefinder_module/serotypefinder_db/kma/compress.h
site-packages/ecoliTyper/modules/serotypefinder_module/serotypefinder_db/kma/compress.o
site-packages/ecoliTyper/modules/serotypefinder_module/serotypefinder_db/kma/conclave.c
site-packages/ecoliTyper/modules/serotypefinder_module/serotypefinder_db/kma/conclave.h
site-packages/ecoliTyper/modules/serotypefinder_module/serotypefinder_db/kma/conclave.o
site-packages/ecoliTyper/modules/serotypefinder_module/serotypefinder_db/kma/conda/build.sh
site-packages/ecoliTyper/modules/serotypefinder_module/serotypefinder_db/kma/conda/make_conda.py
site-packages/ecoliTyper/modules/serotypefinder_module/serotypefinder_db/kma/conda/make_conda_no_arch.py
site-packages/ecoliTyper/modules/serotypefinder_module/serotypefinder_db/kma/db.c
site-packages/ecoliTyper/modules/serotypefinder_module/serotypefinder_db/kma/db.h
site-packages/ecoliTyper/modules/serotypefinder_module/serotypefinder_db/kma/db.o
site-packages/ecoliTyper/modules/serotypefinder_module/serotypefinder_db/kma/decon.c
site-packages/ecoliTyper/modules/serotypefinder_module/serotypefinder_db/kma/decon.h
site-packages/ecoliTyper/modules/serotypefinder_module/serotypefinder_db/kma/decon.o
site-packages/ecoliTyper/modules/serotypefinder_module/serotypefinder_db/kma/dist.c
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site-packages/ecoliTyper/modules/serotypefinder_module/serotypefinder_db/kma/dist.o
site-packages/ecoliTyper/modules/serotypefinder_module/serotypefinder_db/kma/ef.c
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site-packages/ecoliTyper/modules/serotypefinder_module/serotypefinder_db/kma/envs/linux-build.yml
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site-packages/ecoliTyper/modules/serotypefinder_module/serotypefinder_db/kma/filebuff.c
site-packages/ecoliTyper/modules/serotypefinder_module/serotypefinder_db/kma/filebuff.h
site-packages/ecoliTyper/modules/serotypefinder_module/serotypefinder_db/kma/filebuff.o
site-packages/ecoliTyper/modules/serotypefinder_module/serotypefinder_db/kma/frags.c
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site-packages/ecoliTyper/modules/serotypefinder_module/serotypefinder_db/kma/frags.o
site-packages/ecoliTyper/modules/serotypefinder_module/serotypefinder_db/kma/fuzzymatch.c
site-packages/ecoliTyper/modules/serotypefinder_module/serotypefinder_db/kma/hashmap.c
site-packages/ecoliTyper/modules/serotypefinder_module/serotypefinder_db/kma/hashmap.h
site-packages/ecoliTyper/modules/serotypefinder_module/serotypefinder_db/kma/hashmap.o
site-packages/ecoliTyper/modules/serotypefinder_module/serotypefinder_db/kma/hashmapcci.c
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site-packages/ecoliTyper/modules/serotypefinder_module/serotypefinder_db/kma/hashmapcci.o
site-packages/ecoliTyper/modules/serotypefinder_module/serotypefinder_db/kma/hashmapindex.c
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site-packages/ecoliTyper/modules/serotypefinder_module/serotypefinder_db/kma/hashmapkma.c
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site-packages/ecoliTyper/modules/serotypefinder_module/serotypefinder_db/kma/hashmapkmers.c
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site-packages/ecoliTyper/modules/serotypefinder_module/serotypefinder_db/kma/kma_update.c
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