├── .gitignore ├── CHANGELOG ├── ConfigTemplate.csv ├── DS_baseSchema.yaml ├── LICENSE.md ├── README.html ├── README.md ├── ResetSnakefile ├── Snakefile ├── VERSION ├── ambiguity_codes.txt ├── envs ├── DS_env_full.yaml └── DS_env_recovery.yaml ├── scripts ├── BamToMutposVCF.py ├── BedParser.py ├── DepthSummaryCsv.py ├── MakeDepthPlot.R ├── Mask_VCF.py ├── MutationFreqFromVCF.py ├── NearIndelFilt.py ├── RecoveryScripts │ ├── noRecovery.sh │ ├── recoverAll.sh │ ├── recoverAmbig.sh │ └── recoverWrongSpecies.sh ├── SNP_finder.py ├── SNP_finder_dev.py ├── UnifiedConsensusMaker.py ├── VCF_Parser.py ├── VarDictMpC.py ├── VarDictToVCF.py ├── blastFilter.py ├── blastMonitor.py ├── countAmbiguityClasses.py ├── countMutsPerCycle.py ├── makeDepthFile.py ├── makeSnpList.py ├── mergeSubImages.py ├── plotInsertSize.R ├── plotSummaryDepth.py ├── plotSummaryFamilySize.R ├── plotSummaryInsertSize.py ├── plotSummaryMutsByCycle.R ├── postBlastFilter.py ├── retrieveSummary.py ├── setupR.R └── tiff2png.py ├── setupBlastDb ├── AddTaxonID.py └── blastDbSetup.sh ├── setupDS.sh └── test ├── expectedReports ├── test1.expectedReport.html ├── test2.expectedReport.html ├── test3.expectedReport.html ├── test4.expectedReport.html ├── test5.expectedReport.html └── test6.expectedReport.html ├── resetTest.sh ├── testBlastDb ├── testBlastDb.nal ├── testBlastDbSrc_hg38.fa ├── testBlastDbSrc_rheMac10.fa ├── test_hg38.nhr ├── test_hg38.nin ├── test_hg38.nsq ├── test_rheMac10.nhr ├── test_rheMac10.nin └── test_rheMac10.nsq ├── testData ├── testSeq1.fastq.gz └── testSeq2.fastq.gz ├── testRef ├── testRef.dict ├── testRef.fa ├── testRef.fa.amb ├── testRef.fa.ann ├── testRef.fa.bwt ├── testRef.fa.fai ├── testRef.fa.pac └── testRef.fa.sa └── testTarget └── test.bed /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Kennedy-Lab-UW/Duplex-Seq-Pipeline/HEAD/.gitignore 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