LICENSE
MANIFEST.in
setup.py
genemethods/__init__.py
genemethods/version.py
genemethods.egg-info/PKG-INFO
genemethods.egg-info/SOURCES.txt
genemethods.egg-info/dependency_links.txt
genemethods.egg-info/entry_points.txt
genemethods.egg-info/top_level.txt
genemethods/MASHsippr/__init__.py
genemethods/MASHsippr/mash.py
genemethods/MASHsippr/mashsippr.py
genemethods/MLST/__init__.py
genemethods/MLST/mlst_kma.py
genemethods/MLSTsippr/__init__.py
genemethods/MLSTsippr/mlst.py
genemethods/MLSTsippr/sipprmlst.py
genemethods/SequenceExtractor/__init__.py
genemethods/SequenceExtractor/src/__init__.py
genemethods/SequenceExtractor/src/sequenceExtractor.py
genemethods/SequenceExtractor/tests/__init__.py
genemethods/SequenceExtractor/tests/test_sequence_extractor.py
genemethods/SequenceExtractor/tests/fastadetails/iseqid_vcontig_vstart_vstop.txt
genemethods/SequenceExtractor/tests/fastadetails/vseqid_icontig_vstart_vstop.txt
genemethods/SequenceExtractor/tests/fastadetails/vseqid_vcontig_istart_vstop.txt
genemethods/SequenceExtractor/tests/fastadetails/vseqid_vcontig_nstart_vstop.txt
genemethods/SequenceExtractor/tests/fastadetails/vseqid_vcontig_rstart_rstop.txt
genemethods/SequenceExtractor/tests/fastadetails/vseqid_vcontig_vstart_bstop.txt
genemethods/SequenceExtractor/tests/fastadetails/vseqid_vcontig_vstart_mstop.txt
genemethods/SequenceExtractor/tests/fastadetails/vseqid_vcontig_vstart_vstop.txt
genemethods/SequenceExtractor/tests/fastadetails/vseqid_vcontig_vstart_vstop_2_same_contig.txt
genemethods/SequenceExtractor/tests/fastadetails/vseqid_vcontig_vstart_vstop_2_same_contig_overlap.txt
genemethods/SequenceExtractor/tests/fastadetails/vseqid_vcontig_vstart_vstop_2_same_contig_reversed.txt
genemethods/SequenceExtractor/tests/fastadetails/vseqid_vcontig_vstart_vstop_2_separate_contigs.txt
genemethods/SequenceExtractor/tests/fastadetails/vseqid_vcontig_vstart_vstop_2_seqids.txt
genemethods/SequenceExtractor/tests/fastadetails/vseqid_vcontig_vstart_vstop_2_seqids_full_contig.txt
genemethods/SequenceExtractor/tests/fastadetails/vseqid_vcontig_vstart_vstop_2_seqids_multiple.txt
genemethods/SequenceExtractor/tests/fastadetails/vseqid_vcontig_vstart_vstop_2_seqids_multiple_invalid.txt
genemethods/SequenceExtractor/tests/fastadetails/vseqid_vcontig_vstart_vstop_idelimiter.txt
genemethods/SequenceExtractor/tests/sequences/2019-SEQ-0848.fasta
genemethods/SequenceExtractor/tests/sequences/2019-SEQ-1019.fasta
genemethods/assemblypipeline/CHAS.py
genemethods/assemblypipeline/GeneSeekr.py
genemethods/assemblypipeline/GeneSeekr_tblastx.py
genemethods/assemblypipeline/__init__.py
genemethods/assemblypipeline/assembly_evaluation.py
genemethods/assemblypipeline/basicAssembly.py
genemethods/assemblypipeline/bowtie.py
genemethods/assemblypipeline/compress.py
genemethods/assemblypipeline/createobject.py
genemethods/assemblypipeline/ec_typer.py
genemethods/assemblypipeline/errorcorrection.py
genemethods/assemblypipeline/fastqCreator.py
genemethods/assemblypipeline/fastqmover.py
genemethods/assemblypipeline/fileprep.py
genemethods/assemblypipeline/getmlst.py
genemethods/assemblypipeline/ipcress_format_subtyping_primers.txt
genemethods/assemblypipeline/ipcress_format_subtyping_primers_degenerate.txt
genemethods/assemblypipeline/legacy_vtyper.py
genemethods/assemblypipeline/mMLST.py
genemethods/assemblypipeline/metadataReader.py
genemethods/assemblypipeline/mobrecon.py
genemethods/assemblypipeline/offhours.py
genemethods/assemblypipeline/phix.py
genemethods/assemblypipeline/plasmidfinder.py
genemethods/assemblypipeline/primer_finder_bbduk.py
genemethods/assemblypipeline/primer_finder_ipcress.py
genemethods/assemblypipeline/primer_finder_ultimatum.py
genemethods/assemblypipeline/primers.txt
genemethods/assemblypipeline/prodigal.py
genemethods/assemblypipeline/prophages.py
genemethods/assemblypipeline/quality.py
genemethods/assemblypipeline/quaster.py
genemethods/assemblypipeline/reporter.py
genemethods/assemblypipeline/runMetadata.py
genemethods/assemblypipeline/seqsero.py
genemethods/assemblypipeline/serotype.py
genemethods/assemblypipeline/sistr.py
genemethods/assemblypipeline/sixteenS.py
genemethods/assemblypipeline/skesa.py
genemethods/assemblypipeline/spadesRun.py
genemethods/assemblypipeline/ssi_subtyping_primers.txt
genemethods/assemblypipeline/univec.py
genemethods/assemblypipeline/versions.py
genemethods/assemblypipeline/virulence.py
genemethods/assemblypipeline/vtx_subtyping_primers.txt
genemethods/assemblypipeline/vtyper.py
genemethods/assemblypipeline/ePCR/e-PCR
genemethods/assemblypipeline/ePCR/fahash
genemethods/assemblypipeline/ePCR/famap
genemethods/assemblypipeline/ePCR/re-PCR
genemethods/cgecore/__init__.py
genemethods/cgecore/alignment.py
genemethods/cgecore/argumentparsing.py
genemethods/cgecore/cgefinder.py
genemethods/cgecore/cmdline.py
genemethods/cgecore/setup.py
genemethods/cgecore/utility.py
genemethods/cgecore/blaster/__init__.py
genemethods/cgecore/blaster/blaster.py
genemethods/cgecore/blaster/run_blaster.py
genemethods/coreGenome/__init__.py
genemethods/coreGenome/annotate.py
genemethods/coreGenome/core.py
genemethods/coreGenome/coretyper.py
genemethods/customsippr/__init__.py
genemethods/customsippr/customsippr.py
genemethods/gdcs/__init__.py
genemethods/gdcs/gdcs.py
genemethods/geneseekr/__init__.py
genemethods/geneseekr/blast.py
genemethods/geneseekr/geneseekr.py
genemethods/geneseekr/kma.py
genemethods/geneseekr/parser.py
genemethods/genesippr/__init__.py
genemethods/genesippr/genesippr.py
genemethods/pointfinder/PointFinder.py
genemethods/pointfinder/__init__.py
genemethods/pointsippr/__init__.py
genemethods/pointsippr/pointsippr.py
genemethods/serosippr/__init__.py
genemethods/serosippr/serosippr.py
genemethods/sipprCommon/__init__.py
genemethods/sipprCommon/bowtie.py
genemethods/sipprCommon/createObject.py
genemethods/sipprCommon/create_sample_sheet.py
genemethods/sipprCommon/database.py
genemethods/sipprCommon/editsamheaders.py
genemethods/sipprCommon/fastqCreator.py
genemethods/sipprCommon/kma_wrapper.py
genemethods/sipprCommon/objectprep.py
genemethods/sipprCommon/offhours.py
genemethods/sipprCommon/runMetadata.py
genemethods/sipprCommon/sippingmethods.py
genemethods/sipprverse_reporter/__init__.py
genemethods/sipprverse_reporter/reports.py
genemethods/sixteenS/__init__.py
genemethods/sixteenS/sixteens_full.py
genemethods/typingclasses/__init__.py
genemethods/typingclasses/resistance.py
genemethods/typingclasses/typingclasses.py