bin/a_sample_mt.sh
bin/addadapters.sh
bin/addssu.sh
bin/adjusthomopolymers.sh
bin/alignrandom.sh
bin/alltoall.sh
bin/analyzeaccession.sh
bin/analyzegenes.sh
bin/analyzesketchresults.sh
bin/applyvariants.sh
bin/bamlinestreamer.sh
bin/bandedaligner.sh
bin/bandedplusaligner.sh
bin/bbcms.sh
bin/bbcountunique.sh
bin/bbcrisprfinder.sh
bin/bbduk.sh
bin/bbdukOld.sh
bin/bbdukS.sh
bin/bbest.sh
bin/bbfakereads.sh
bin/bbmap.sh
bin/bbmapskimmer.sh
bin/bbmask.sh
bin/bbmerge-auto.sh
bin/bbmerge.sh
bin/bbnorm.sh
bin/bbrealign.sh
bin/bbrename.sh
bin/bbsketch.sh
bin/bbsort.sh
bin/bbsplit.sh
bin/bbsplitpairs.sh
bin/bbstats.sh
bin/bbversion.sh
bin/bbwrap.sh
bin/bloomfilter.sh
bin/bloomfilterparser.sh
bin/build_env_setup.sh
bin/calcmem.sh
bin/calctruequality.sh
bin/callgenes.sh
bin/callpeaks.sh
bin/callvariants.sh
bin/callvariants2.sh
bin/cat.sh
bin/cbcl2text.sh
bin/cg2illumina.sh
bin/checkstrand.sh
bin/cladeloader.sh
bin/cladeserver.sh
bin/cloudplot.sh
bin/clumpify.sh
bin/commonkmers.sh
bin/comparegff.sh
bin/comparelabels.sh
bin/comparesketch.sh
bin/comparessu.sh
bin/comparevcf.sh
bin/conda_build.sh
bin/consect.sh
bin/consensus.sh
bin/copyfile.sh
bin/countbarcodes.sh
bin/countbarcodes2.sh
bin/countduplicates.sh
bin/countgc.sh
bin/countsharedlines.sh
bin/covmaker.sh
bin/crossblock.sh
bin/crosscontaminate.sh
bin/crosscutaligner.sh
bin/cutgff.sh
bin/cutprimers.sh
bin/decontaminate.sh
bin/dedupe.sh
bin/dedupe2.sh
bin/dedupebymapping.sh
bin/demuxbyname.sh
bin/demuxserver.sh
bin/diskbench.sh
bin/driftingaligner.sh
bin/driftingplusaligner.sh
bin/estherfilter.sh
bin/explodetree.sh
bin/fastqscan.sh
bin/fetchproks.sh
bin/filescan.sh
bin/filterassemblysummary.sh
bin/filterbarcodes.sh
bin/filterbycoverage.sh
bin/filterbyname.sh
bin/filterbysequence.sh
bin/filterbytaxa.sh
bin/filterbytile.sh
bin/filterlines.sh
bin/filtersam.sh
bin/filtersilva.sh
bin/filtersubs.sh
bin/filtervcf.sh
bin/findrepeats.sh
bin/fix_script_paths.sh
bin/fixgaps.sh
bin/fungalrelease.sh
bin/fuse.sh
bin/gbff2gff.sh
bin/getreads.sh
bin/gi2ancestors.sh
bin/gi2taxid.sh
bin/gitable.sh
bin/glocalaligner.sh
bin/gradebins.sh
bin/grademerge.sh
bin/gradesam.sh
bin/icecreamfinder.sh
bin/icecreamgrader.sh
bin/icecreammaker.sh
bin/idmatrix.sh
bin/idtree.sh
bin/indelfree.sh
bin/invertkey.sh
bin/javasetup.sh
bin/kapastats.sh
bin/kcompress.sh
bin/keepbestcopy.sh
bin/khist.sh
bin/kmercountexact.sh
bin/kmercountmulti.sh
bin/kmercountshort.sh
bin/kmercoverage.sh
bin/kmerfilterset.sh
bin/kmerlimit.sh
bin/kmerlimit2.sh
bin/kmerposition.sh
bin/kmutate.sh
bin/lilypad.sh
bin/loadreads.sh
bin/loglog.sh
bin/makechimeras.sh
bin/makecontaminatedgenomes.sh
bin/makepolymers.sh
bin/makequickbinvector.sh
bin/mapPacBio.sh
bin/matrixtocolumns.sh
bin/memdetect.sh
bin/mergeOTUs.sh
bin/mergebarcodes.sh
bin/mergepgm.sh
bin/mergeribo.sh
bin/mergesam.sh
bin/mergesketch.sh
bin/mergesorted.sh
bin/microalign.sh
bin/msa.sh
bin/mutate.sh
bin/muxbyname.sh
bin/netfilter.sh
bin/novademux.sh
bin/parallelogram.sh
bin/partition.sh
bin/phylip2fasta.sh
bin/picksubset.sh
bin/pileup.sh
bin/pileup2.sh
bin/plotflowcell.sh
bin/plotgc.sh
bin/plothist.sh
bin/plotreadposition.sh
bin/polyfilter.sh
bin/postfilter.sh
bin/printtime.sh
bin/processfrag.sh
bin/processhi-c.sh
bin/processspeed.sh
bin/profile.sh
bin/quabblealigner.sh
bin/quantumaligner.sh
bin/quickbin.sh
bin/quickclade.sh
bin/randomgenome.sh
bin/randomreads.sh
bin/randomreadsmg.sh
bin/readlength.sh
bin/reassemble.sh
bin/reducecolumns.sh
bin/reducesilva.sh
bin/reformat.sh
bin/reformat2.sh
bin/reformat3.sh
bin/reformatpb.sh
bin/removebadbarcodes.sh
bin/removecatdogmousehuman.sh
bin/removehuman.sh
bin/removehuman2.sh
bin/removemicrobes.sh
bin/removesmartbell.sh
bin/rename.sh
bin/renamebymapping.sh
bin/renamebysketch.sh
bin/renameimg.sh
bin/renameref.sh
bin/repair.sh
bin/replaceheaders.sh
bin/representative.sh
bin/rqcfilter.sh
bin/rqcfilter2.sh
bin/rqcfilter3.sh
bin/runhmm.sh
bin/samstreamer.sh
bin/samtoroc.sh
bin/scalarintervals.sh
bin/scalars.sh
bin/scoresequence.sh
bin/scrabblealigner.sh
bin/seal.sh
bin/sendclade.sh
bin/sendsketch.sh
bin/seqtovec.sh
bin/shred.sh
bin/shrinkaccession.sh
bin/shuffle.sh
bin/shuffle2.sh
bin/sketch.sh
bin/sketchblacklist.sh
bin/sketchblacklist2.sh
bin/smithwaterman.sh
bin/sortbyname.sh
bin/splitbytaxa.sh
bin/splitnextera.sh
bin/splitribo.sh
bin/splitsam.sh
bin/splitsam4way.sh
bin/splitsam6way.sh
bin/stats.sh
bin/stats3.sh
bin/statswrapper.sh
bin/stream.sh
bin/streamsam.sh
bin/subsketch.sh
bin/summarizecontam.sh
bin/summarizecoverage.sh
bin/summarizecrossblock.sh
bin/summarizemerge.sh
bin/summarizequast.sh
bin/summarizescafstats.sh
bin/summarizeseal.sh
bin/summarizesketch.sh
bin/synthmda.sh
bin/tadpipe.sh
bin/tadpole.sh
bin/tadwrapper.sh
bin/tagandmerge.sh
bin/taxonomy.sh
bin/taxserver.sh
bin/taxsize.sh
bin/taxtree.sh
bin/testaligners.sh
bin/testaligners2.sh
bin/testfilesystem.sh
bin/testformat.sh
bin/testformat2.sh
bin/tetramerfreq.sh
bin/textfile.sh
bin/tiledump.sh
bin/train.sh
bin/translate6frames.sh
bin/trimcontigs.sh
bin/unicode2ascii.sh
bin/unzip.sh
bin/vcf2gff.sh
bin/visualizealignment.sh
bin/wavefrontaligner.sh
bin/wavefrontalignerviz.sh
bin/webcheck.sh
bin/wobblealigner.sh
bin/wobbleplusaligner.sh
bin/xdrophaligner.sh
bin/zz_rename_package.sh
opt/bbmap-39.76-0/README.md
opt/bbmap-39.76-0/a_sample_mt.sh
opt/bbmap-39.76-0/addadapters.sh
opt/bbmap-39.76-0/addssu.sh
opt/bbmap-39.76-0/adjusthomopolymers.sh
opt/bbmap-39.76-0/alignrandom.sh
opt/bbmap-39.76-0/alltoall.sh
opt/bbmap-39.76-0/analyzeaccession.sh
opt/bbmap-39.76-0/analyzegenes.sh
opt/bbmap-39.76-0/analyzesketchresults.sh
opt/bbmap-39.76-0/applyvariants.sh
opt/bbmap-39.76-0/bamlinestreamer.sh
opt/bbmap-39.76-0/bandedaligner.sh
opt/bbmap-39.76-0/bandedplusaligner.sh
opt/bbmap-39.76-0/bbcms.sh
opt/bbmap-39.76-0/bbcountunique.sh
opt/bbmap-39.76-0/bbcrisprfinder.sh
opt/bbmap-39.76-0/bbduk.sh
opt/bbmap-39.76-0/bbdukOld.sh
opt/bbmap-39.76-0/bbdukS.sh
opt/bbmap-39.76-0/bbest.sh
opt/bbmap-39.76-0/bbfakereads.sh
opt/bbmap-39.76-0/bbmap.sh
opt/bbmap-39.76-0/bbmapskimmer.sh
opt/bbmap-39.76-0/bbmask.sh
opt/bbmap-39.76-0/bbmerge-auto.sh
opt/bbmap-39.76-0/bbmerge.sh
opt/bbmap-39.76-0/bbnorm.sh
opt/bbmap-39.76-0/bbrealign.sh
opt/bbmap-39.76-0/bbrename.sh
opt/bbmap-39.76-0/bbsketch.sh
opt/bbmap-39.76-0/bbsort.sh
opt/bbmap-39.76-0/bbsplit.sh
opt/bbmap-39.76-0/bbsplitpairs.sh
opt/bbmap-39.76-0/bbstats.sh
opt/bbmap-39.76-0/bbtools.jar
opt/bbmap-39.76-0/bbversion.sh
opt/bbmap-39.76-0/bbwrap.sh
opt/bbmap-39.76-0/bitbucket-pipelines.yml
opt/bbmap-39.76-0/bloomfilter.sh
opt/bbmap-39.76-0/bloomfilterparser.sh
opt/bbmap-39.76-0/build.xml
opt/bbmap-39.76-0/build_env_setup.sh
opt/bbmap-39.76-0/calcmem.sh
opt/bbmap-39.76-0/calctruequality.sh
opt/bbmap-39.76-0/callgenes.sh
opt/bbmap-39.76-0/callpeaks.sh
opt/bbmap-39.76-0/callvariants.sh
opt/bbmap-39.76-0/callvariants2.sh
opt/bbmap-39.76-0/cat.sh
opt/bbmap-39.76-0/cbcl2text.sh
opt/bbmap-39.76-0/cg2illumina.sh
opt/bbmap-39.76-0/checkstrand.sh
opt/bbmap-39.76-0/cladeloader.sh
opt/bbmap-39.76-0/cladeserver.sh
opt/bbmap-39.76-0/cloudplot.sh
opt/bbmap-39.76-0/clumpify.sh
opt/bbmap-39.76-0/commonkmers.sh
opt/bbmap-39.76-0/comparegff.sh
opt/bbmap-39.76-0/comparelabels.sh
opt/bbmap-39.76-0/comparesketch.sh
opt/bbmap-39.76-0/comparessu.sh
opt/bbmap-39.76-0/comparevcf.sh
opt/bbmap-39.76-0/conda_build.sh
opt/bbmap-39.76-0/config/cluster16s.txt
opt/bbmap-39.76-0/config/filter16s.txt
opt/bbmap-39.76-0/config/histograms.txt
opt/bbmap-39.76-0/config/recalibrate.txt
opt/bbmap-39.76-0/config/rnaseq.txt
opt/bbmap-39.76-0/config/trimadapters.txt
opt/bbmap-39.76-0/consect.sh
opt/bbmap-39.76-0/consensus.sh
opt/bbmap-39.76-0/copyfile.sh
opt/bbmap-39.76-0/countbarcodes.sh
opt/bbmap-39.76-0/countbarcodes2.sh
opt/bbmap-39.76-0/countduplicates.sh
opt/bbmap-39.76-0/countgc.sh
opt/bbmap-39.76-0/countsharedlines.sh
opt/bbmap-39.76-0/covmaker.sh
opt/bbmap-39.76-0/crossblock.sh
opt/bbmap-39.76-0/crosscontaminate.sh
opt/bbmap-39.76-0/crosscutaligner.sh
opt/bbmap-39.76-0/cutgff.sh
opt/bbmap-39.76-0/cutprimers.sh
opt/bbmap-39.76-0/decontaminate.sh
opt/bbmap-39.76-0/dedupe.sh
opt/bbmap-39.76-0/dedupe2.sh
opt/bbmap-39.76-0/dedupebymapping.sh
opt/bbmap-39.76-0/demuxbyname.sh
opt/bbmap-39.76-0/demuxserver.sh
opt/bbmap-39.76-0/diskbench.sh
opt/bbmap-39.76-0/docs/BBTools_List.txt
opt/bbmap-39.76-0/docs/Legal.txt
opt/bbmap-39.76-0/docs/Legal_Illumina.txt
opt/bbmap-39.76-0/docs/RestartingServers.txt
opt/bbmap-39.76-0/docs/TableOfContents.txt
opt/bbmap-39.76-0/docs/ToolDescriptions.txt
opt/bbmap-39.76-0/docs/UsageGuide.txt
opt/bbmap-39.76-0/docs/bbcms.txt
opt/bbmap-39.76-0/docs/changelog.txt
opt/bbmap-39.76-0/docs/citation.txt
opt/bbmap-39.76-0/docs/compiling.txt
opt/bbmap-39.76-0/docs/git.txt
opt/bbmap-39.76-0/docs/guides/A_SampleGuide.txt
opt/bbmap-39.76-0/docs/guides/AddAdaptersGuide.txt
opt/bbmap-39.76-0/docs/guides/BBDukGuide.txt
opt/bbmap-39.76-0/docs/guides/BBMapGuide.txt
opt/bbmap-39.76-0/docs/guides/BBMap_old_readme.txt
opt/bbmap-39.76-0/docs/guides/BBMaskGuide.txt
opt/bbmap-39.76-0/docs/guides/BBMergeGuide.txt
opt/bbmap-39.76-0/docs/guides/BBNormGuide.txt
opt/bbmap-39.76-0/docs/guides/BBSketchGuide.txt
opt/bbmap-39.76-0/docs/guides/CalcUniquenessGuide.txt
opt/bbmap-39.76-0/docs/guides/CallVariantsGuide.txt
opt/bbmap-39.76-0/docs/guides/ClumpifyGuide.txt
opt/bbmap-39.76-0/docs/guides/DedupeGuide.txt
opt/bbmap-39.76-0/docs/guides/FilterByTileGuide.txt
opt/bbmap-39.76-0/docs/guides/PreprocessingGuide.txt
opt/bbmap-39.76-0/docs/guides/ReformatGuide.txt
opt/bbmap-39.76-0/docs/guides/RepairGuide.txt
opt/bbmap-39.76-0/docs/guides/SealGuide.txt
opt/bbmap-39.76-0/docs/guides/SplitNexteraGuide.txt
opt/bbmap-39.76-0/docs/guides/StatsGuide.txt
opt/bbmap-39.76-0/docs/guides/TadpoleGuide.txt
opt/bbmap-39.76-0/docs/guides/TaxonomyGuide.txt
opt/bbmap-39.76-0/docs/readme.txt
opt/bbmap-39.76-0/docs/readme_config.txt
opt/bbmap-39.76-0/docs/readme_filetypes.txt
opt/bbmap-39.76-0/driftingaligner.sh
opt/bbmap-39.76-0/driftingplusaligner.sh
opt/bbmap-39.76-0/estherfilter.sh
opt/bbmap-39.76-0/explodetree.sh
opt/bbmap-39.76-0/fastqscan.sh
opt/bbmap-39.76-0/fetchproks.sh
opt/bbmap-39.76-0/filescan.sh
opt/bbmap-39.76-0/filterassemblysummary.sh
opt/bbmap-39.76-0/filterbarcodes.sh
opt/bbmap-39.76-0/filterbycoverage.sh
opt/bbmap-39.76-0/filterbyname.sh
opt/bbmap-39.76-0/filterbysequence.sh
opt/bbmap-39.76-0/filterbytaxa.sh
opt/bbmap-39.76-0/filterbytile.sh
opt/bbmap-39.76-0/filterlines.sh
opt/bbmap-39.76-0/filtersam.sh
opt/bbmap-39.76-0/filtersilva.sh
opt/bbmap-39.76-0/filtersubs.sh
opt/bbmap-39.76-0/filtervcf.sh
opt/bbmap-39.76-0/findrepeats.sh
opt/bbmap-39.76-0/fix_script_paths.sh
opt/bbmap-39.76-0/fixgaps.sh
opt/bbmap-39.76-0/fungalrelease.sh
opt/bbmap-39.76-0/fuse.sh
opt/bbmap-39.76-0/gbff2gff.sh
opt/bbmap-39.76-0/getreads.sh
opt/bbmap-39.76-0/gi2ancestors.sh
opt/bbmap-39.76-0/gi2taxid.sh
opt/bbmap-39.76-0/gitable.sh
opt/bbmap-39.76-0/glocalaligner.sh
opt/bbmap-39.76-0/gradebins.sh
opt/bbmap-39.76-0/grademerge.sh
opt/bbmap-39.76-0/gradesam.sh
opt/bbmap-39.76-0/icecreamfinder.sh
opt/bbmap-39.76-0/icecreamgrader.sh
opt/bbmap-39.76-0/icecreammaker.sh
opt/bbmap-39.76-0/idmatrix.sh
opt/bbmap-39.76-0/idtree.sh
opt/bbmap-39.76-0/indelfree.sh
opt/bbmap-39.76-0/invertkey.sh
opt/bbmap-39.76-0/javasetup.sh
opt/bbmap-39.76-0/jni/BBMergeOverlapper.c
opt/bbmap-39.76-0/jni/BBMergeOverlapper.o
opt/bbmap-39.76-0/jni/BandedAlignerJNI.c
opt/bbmap-39.76-0/jni/BandedAlignerJNI.o
opt/bbmap-39.76-0/jni/CMakeLists.txt
opt/bbmap-39.76-0/jni/IceCreamAlignerJNI.c
opt/bbmap-39.76-0/jni/IceCreamAlignerJNI.o
opt/bbmap-39.76-0/jni/MultiStateAligner11tsJNI.c
opt/bbmap-39.76-0/jni/MultiStateAligner11tsJNI.o
opt/bbmap-39.76-0/jni/README.txt
opt/bbmap-39.76-0/jni/align2_BandedAlignerJNI.h
opt/bbmap-39.76-0/jni/align2_MultiStateAligner11tsJNI.h
opt/bbmap-39.76-0/jni/icecream_IceCreamAlignerJNI.h
opt/bbmap-39.76-0/jni/jgi_BBMergeOverlapper.h
opt/bbmap-39.76-0/jni/libbbtoolsjni.dylib
opt/bbmap-39.76-0/jni/libbbtoolsjni.so
opt/bbmap-39.76-0/jni/makefile.linux
opt/bbmap-39.76-0/jni/makefile.osx
opt/bbmap-39.76-0/jni/run.sh
opt/bbmap-39.76-0/kapastats.sh
opt/bbmap-39.76-0/kcompress.sh
opt/bbmap-39.76-0/keepbestcopy.sh
opt/bbmap-39.76-0/khist.sh
opt/bbmap-39.76-0/kmercountexact.sh
opt/bbmap-39.76-0/kmercountmulti.sh
opt/bbmap-39.76-0/kmercountshort.sh
opt/bbmap-39.76-0/kmercoverage.sh
opt/bbmap-39.76-0/kmerfilterset.sh
opt/bbmap-39.76-0/kmerlimit.sh
opt/bbmap-39.76-0/kmerlimit2.sh
opt/bbmap-39.76-0/kmerposition.sh
opt/bbmap-39.76-0/kmutate.sh
opt/bbmap-39.76-0/license.txt
opt/bbmap-39.76-0/lilypad.sh
opt/bbmap-39.76-0/loadreads.sh
opt/bbmap-39.76-0/loglog.sh
opt/bbmap-39.76-0/makechimeras.sh
opt/bbmap-39.76-0/makecontaminatedgenomes.sh
opt/bbmap-39.76-0/makepolymers.sh
opt/bbmap-39.76-0/makequickbinvector.sh
opt/bbmap-39.76-0/mapPacBio.sh
opt/bbmap-39.76-0/matrixtocolumns.sh
opt/bbmap-39.76-0/memdetect.sh
opt/bbmap-39.76-0/mergeOTUs.sh
opt/bbmap-39.76-0/mergebarcodes.sh
opt/bbmap-39.76-0/mergepgm.sh
opt/bbmap-39.76-0/mergeribo.sh
opt/bbmap-39.76-0/mergesam.sh
opt/bbmap-39.76-0/mergesketch.sh
opt/bbmap-39.76-0/mergesorted.sh
opt/bbmap-39.76-0/metadata_conda_debug.yaml
opt/bbmap-39.76-0/microalign.sh
opt/bbmap-39.76-0/msa.sh
opt/bbmap-39.76-0/mutate.sh
opt/bbmap-39.76-0/muxbyname.sh
opt/bbmap-39.76-0/netfilter.sh
opt/bbmap-39.76-0/novademux.sh
opt/bbmap-39.76-0/parallelogram.sh
opt/bbmap-39.76-0/partition.sh
opt/bbmap-39.76-0/phylip2fasta.sh
opt/bbmap-39.76-0/picksubset.sh
opt/bbmap-39.76-0/pileup.sh
opt/bbmap-39.76-0/pileup2.sh
opt/bbmap-39.76-0/pipelines/assembleMito_Illumina.sh
opt/bbmap-39.76-0/pipelines/assembleMito_PacBio.sh
opt/bbmap-39.76-0/pipelines/assemble_polyg_isolate_v1.sh
opt/bbmap-39.76-0/pipelines/assemble_polyg_meta_v1.sh
opt/bbmap-39.76-0/pipelines/assemblyPipeline.sh
opt/bbmap-39.76-0/pipelines/callInsertions.sh
opt/bbmap-39.76-0/pipelines/covid/makeSummary.sh
opt/bbmap-39.76-0/pipelines/covid/processCorona.sh
opt/bbmap-39.76-0/pipelines/covid/processCoronaWrapper.sh
opt/bbmap-39.76-0/pipelines/covid/readme.txt
opt/bbmap-39.76-0/pipelines/covid/recal.sh
opt/bbmap-39.76-0/pipelines/crisprPipeline.sh
opt/bbmap-39.76-0/pipelines/cutRna.sh
opt/bbmap-39.76-0/pipelines/fetch/fetchMito.sh
opt/bbmap-39.76-0/pipelines/fetch/fetchNt.sh
opt/bbmap-39.76-0/pipelines/fetch/fetchNtOuter.sh
opt/bbmap-39.76-0/pipelines/fetch/fetchPlasmid.sh
opt/bbmap-39.76-0/pipelines/fetch/fetchPlastid.sh
opt/bbmap-39.76-0/pipelines/fetch/fetchProkByGenus.sh
opt/bbmap-39.76-0/pipelines/fetch/fetchRefSeq.sh
opt/bbmap-39.76-0/pipelines/fetch/fetchRefSeqClades.sh
opt/bbmap-39.76-0/pipelines/fetch/fetchRefSeqCladesOuter.sh
opt/bbmap-39.76-0/pipelines/fetch/fetchSilva.sh
opt/bbmap-39.76-0/pipelines/fetch/fetchTaxonomy.sh
opt/bbmap-39.76-0/pipelines/fetch/runRefSeqProtein.sh
opt/bbmap-39.76-0/pipelines/fetch/sketchRefSeq.sh
opt/bbmap-39.76-0/pipelines/makeRiboKmers.sh
opt/bbmap-39.76-0/pipelines/processIMG.sh
opt/bbmap-39.76-0/pipelines/process_lane_v007.sh
opt/bbmap-39.76-0/pipelines/server/startNtServerVM.sh
opt/bbmap-39.76-0/pipelines/server/startProteinServerVM.sh
opt/bbmap-39.76-0/pipelines/server/startRefseqServerVM.sh
opt/bbmap-39.76-0/pipelines/server/startSilvaServerVM.sh
opt/bbmap-39.76-0/pipelines/server/startTaxServerVM.sh
opt/bbmap-39.76-0/pipelines/silva/fetchSilva.sh
opt/bbmap-39.76-0/pipelines/silva/make15mers.sh
opt/bbmap-39.76-0/pipelines/silva/makeCoveringSetLsu.sh
opt/bbmap-39.76-0/pipelines/silva/makeCoveringSetSsu.sh
opt/bbmap-39.76-0/pipelines/silva/makeRep.sh
opt/bbmap-39.76-0/pipelines/testPlatformQuality.sh
opt/bbmap-39.76-0/pipelines/testsketch.sh
opt/bbmap-39.76-0/pipelines/variantPipeline.sh
opt/bbmap-39.76-0/plotflowcell.sh
opt/bbmap-39.76-0/plotgc.sh
opt/bbmap-39.76-0/plothist.sh
opt/bbmap-39.76-0/plotreadposition.sh
opt/bbmap-39.76-0/polyfilter.sh
opt/bbmap-39.76-0/postfilter.sh
opt/bbmap-39.76-0/printtime.sh
opt/bbmap-39.76-0/processfrag.sh
opt/bbmap-39.76-0/processhi-c.sh
opt/bbmap-39.76-0/processspeed.sh
opt/bbmap-39.76-0/profile.sh
opt/bbmap-39.76-0/quabblealigner.sh
opt/bbmap-39.76-0/quantumaligner.sh
opt/bbmap-39.76-0/quickbin.sh
opt/bbmap-39.76-0/quickclade.sh
opt/bbmap-39.76-0/randomgenome.sh
opt/bbmap-39.76-0/randomreads.sh
opt/bbmap-39.76-0/randomreadsmg.sh
opt/bbmap-39.76-0/readlength.sh
opt/bbmap-39.76-0/reassemble.sh
opt/bbmap-39.76-0/reducecolumns.sh
opt/bbmap-39.76-0/reducesilva.sh
opt/bbmap-39.76-0/reformat.sh
opt/bbmap-39.76-0/reformat2.sh
opt/bbmap-39.76-0/reformat3.sh
opt/bbmap-39.76-0/reformatpb.sh
opt/bbmap-39.76-0/removebadbarcodes.sh
opt/bbmap-39.76-0/removecatdogmousehuman.sh
opt/bbmap-39.76-0/removehuman.sh
opt/bbmap-39.76-0/removehuman2.sh
opt/bbmap-39.76-0/removemicrobes.sh
opt/bbmap-39.76-0/removesmartbell.sh
opt/bbmap-39.76-0/rename.sh
opt/bbmap-39.76-0/renamebymapping.sh
opt/bbmap-39.76-0/renamebysketch.sh
opt/bbmap-39.76-0/renameimg.sh
opt/bbmap-39.76-0/renameref.sh
opt/bbmap-39.76-0/repair.sh
opt/bbmap-39.76-0/replaceheaders.sh
opt/bbmap-39.76-0/representative.sh
opt/bbmap-39.76-0/resources/16S_15mers.fa
opt/bbmap-39.76-0/resources/16S_consensus_sequence.fa
opt/bbmap-39.76-0/resources/18S_15mers.fa
opt/bbmap-39.76-0/resources/18S_consensus_sequence.fa
opt/bbmap-39.76-0/resources/23S_15mers.fa
opt/bbmap-39.76-0/resources/23S_consensus_sequence.fa
opt/bbmap-39.76-0/resources/5S_10mers.fa
opt/bbmap-39.76-0/resources/5S_11mers.fa
opt/bbmap-39.76-0/resources/5S_12mers.fa
opt/bbmap-39.76-0/resources/5S_15mers.fa
opt/bbmap-39.76-0/resources/5S_9mers.fa
opt/bbmap-39.76-0/resources/5S_consensus_sequence.fa
opt/bbmap-39.76-0/resources/Covid19_ref.fa
opt/bbmap-39.76-0/resources/ITS_animal_consensus_sequence.fq
opt/bbmap-39.76-0/resources/ITS_consensus_sequence.fq
opt/bbmap-39.76-0/resources/ITS_fungi_consensus_sequence.fq
opt/bbmap-39.76-0/resources/ITS_nonfungi_consensus_sequence.fq
opt/bbmap-39.76-0/resources/ITS_other_consensus_sequence.fq
opt/bbmap-39.76-0/resources/ITS_plant_consensus_sequence.fq
opt/bbmap-39.76-0/resources/ITS_universal_consensus_sequence.fq
opt/bbmap-39.76-0/resources/PacBioAdapter.fa
opt/bbmap-39.76-0/resources/SIP_spikeins.fa.gz
opt/bbmap-39.76-0/resources/adapters.fa
opt/bbmap-39.76-0/resources/adapters_no_transposase.fa.gz
opt/bbmap-39.76-0/resources/artic3.fasta
opt/bbmap-39.76-0/resources/bbmerge.bbnet
opt/bbmap-39.76-0/resources/blacklist_nt_merged.sketch
opt/bbmap-39.76-0/resources/blacklist_prokprot_merged.sketch
opt/bbmap-39.76-0/resources/blacklist_refseq_merged.sketch
opt/bbmap-39.76-0/resources/blacklist_silva_merged.sketch
opt/bbmap-39.76-0/resources/contents.txt
opt/bbmap-39.76-0/resources/crelox.fa.gz
opt/bbmap-39.76-0/resources/crispr.bbnet.gz
opt/bbmap-39.76-0/resources/crisprs.fa.gz
opt/bbmap-39.76-0/resources/entropy_k4_w150.tsv
opt/bbmap-39.76-0/resources/favicon.ico
opt/bbmap-39.76-0/resources/kapatags.L40.fa
opt/bbmap-39.76-0/resources/lambda.fa.gz
opt/bbmap-39.76-0/resources/lfpe.linker.fa.gz
opt/bbmap-39.76-0/resources/lsu_15mers.fa
opt/bbmap-39.76-0/resources/m16S_consensus_sequence.fa
opt/bbmap-39.76-0/resources/m18S_consensus_sequence.fa
opt/bbmap-39.76-0/resources/minorAlleleCount.txt
opt/bbmap-39.76-0/resources/model.pgm
opt/bbmap-39.76-0/resources/mtst.fa
opt/bbmap-39.76-0/resources/nextera.fa.gz
opt/bbmap-39.76-0/resources/nextera_LMP_adapter.fa.gz
opt/bbmap-39.76-0/resources/nextera_LMP_linker.fa.gz
opt/bbmap-39.76-0/resources/p16S_consensus_sequence.fa
opt/bbmap-39.76-0/resources/pJET1.2.fa
opt/bbmap-39.76-0/resources/phix174_ill.ref.fa.gz
opt/bbmap-39.76-0/resources/phix2.fa.gz
opt/bbmap-39.76-0/resources/phix_adapters.fa
opt/bbmap-39.76-0/resources/phix_adapters.fa.gz
opt/bbmap-39.76-0/resources/polyA.fa.gz
opt/bbmap-39.76-0/resources/polya.fa
opt/bbmap-39.76-0/resources/polyc.fa
opt/bbmap-39.76-0/resources/polyg.fa
opt/bbmap-39.76-0/resources/polyt.fa
opt/bbmap-39.76-0/resources/primes.txt.gz
opt/bbmap-39.76-0/resources/quickbin1D_all.bbnet
opt/bbmap-39.76-0/resources/quickbinND_all.bbnet
opt/bbmap-39.76-0/resources/remote_files.txt
opt/bbmap-39.76-0/resources/remote_files_old.txt
opt/bbmap-39.76-0/resources/sample1.fq.gz
opt/bbmap-39.76-0/resources/sample2.fq.gz
opt/bbmap-39.76-0/resources/sequencing_artifacts.fa.gz
opt/bbmap-39.76-0/resources/short.fa
opt/bbmap-39.76-0/resources/shred4merFractions.tsv
opt/bbmap-39.76-0/resources/ssu_15mers.fa
opt/bbmap-39.76-0/resources/tRNA_10mers.fa
opt/bbmap-39.76-0/resources/tRNA_11mers.fa
opt/bbmap-39.76-0/resources/tRNA_15mers.fa
opt/bbmap-39.76-0/resources/tRNA_16mers.fa
opt/bbmap-39.76-0/resources/tRNA_consensus_sequence.fa
opt/bbmap-39.76-0/resources/tax_server.html
opt/bbmap-39.76-0/resources/truseq.fa.gz
opt/bbmap-39.76-0/resources/truseq_rna.fa.gz
opt/bbmap-39.76-0/rqcfilter.sh
opt/bbmap-39.76-0/rqcfilter2.sh
opt/bbmap-39.76-0/rqcfilter3.sh
opt/bbmap-39.76-0/runhmm.sh
opt/bbmap-39.76-0/samstreamer.sh
opt/bbmap-39.76-0/samtoroc.sh
opt/bbmap-39.76-0/scalarintervals.sh
opt/bbmap-39.76-0/scalars.sh
opt/bbmap-39.76-0/scoresequence.sh
opt/bbmap-39.76-0/scrabblealigner.sh
opt/bbmap-39.76-0/seal.sh
opt/bbmap-39.76-0/sendclade.sh
opt/bbmap-39.76-0/sendsketch.sh
opt/bbmap-39.76-0/seqtovec.sh
opt/bbmap-39.76-0/shred.sh
opt/bbmap-39.76-0/shrinkaccession.sh
opt/bbmap-39.76-0/shuffle.sh
opt/bbmap-39.76-0/shuffle2.sh
opt/bbmap-39.76-0/sketch.sh
opt/bbmap-39.76-0/sketchblacklist.sh
opt/bbmap-39.76-0/sketchblacklist2.sh
opt/bbmap-39.76-0/smithwaterman.sh
opt/bbmap-39.76-0/sortbyname.sh
opt/bbmap-39.76-0/splitbytaxa.sh
opt/bbmap-39.76-0/splitnextera.sh
opt/bbmap-39.76-0/splitribo.sh
opt/bbmap-39.76-0/splitsam.sh
opt/bbmap-39.76-0/splitsam4way.sh
opt/bbmap-39.76-0/splitsam6way.sh
opt/bbmap-39.76-0/stats.sh
opt/bbmap-39.76-0/stats3.sh
opt/bbmap-39.76-0/statswrapper.sh
opt/bbmap-39.76-0/stream.sh
opt/bbmap-39.76-0/streamsam.sh
opt/bbmap-39.76-0/subsketch.sh
opt/bbmap-39.76-0/summarizecontam.sh
opt/bbmap-39.76-0/summarizecoverage.sh
opt/bbmap-39.76-0/summarizecrossblock.sh
opt/bbmap-39.76-0/summarizemerge.sh
opt/bbmap-39.76-0/summarizequast.sh
opt/bbmap-39.76-0/summarizescafstats.sh
opt/bbmap-39.76-0/summarizeseal.sh
opt/bbmap-39.76-0/summarizesketch.sh
opt/bbmap-39.76-0/synthmda.sh
opt/bbmap-39.76-0/tadpipe.sh
opt/bbmap-39.76-0/tadpole.sh
opt/bbmap-39.76-0/tadwrapper.sh
opt/bbmap-39.76-0/tagandmerge.sh
opt/bbmap-39.76-0/taxonomy.sh
opt/bbmap-39.76-0/taxserver.sh
opt/bbmap-39.76-0/taxsize.sh
opt/bbmap-39.76-0/taxtree.sh
opt/bbmap-39.76-0/testaligners.sh
opt/bbmap-39.76-0/testaligners2.sh
opt/bbmap-39.76-0/testfilesystem.sh
opt/bbmap-39.76-0/testformat.sh
opt/bbmap-39.76-0/testformat2.sh
opt/bbmap-39.76-0/tetramerfreq.sh
opt/bbmap-39.76-0/textfile.sh
opt/bbmap-39.76-0/tiledump.sh
opt/bbmap-39.76-0/train.sh
opt/bbmap-39.76-0/translate6frames.sh
opt/bbmap-39.76-0/trimcontigs.sh
opt/bbmap-39.76-0/unicode2ascii.sh
opt/bbmap-39.76-0/unzip.sh
opt/bbmap-39.76-0/vcf2gff.sh
opt/bbmap-39.76-0/visualizealignment.sh
opt/bbmap-39.76-0/wavefrontaligner.sh
opt/bbmap-39.76-0/wavefrontalignerviz.sh
opt/bbmap-39.76-0/webcheck.sh
opt/bbmap-39.76-0/wobblealigner.sh
opt/bbmap-39.76-0/wobbleplusaligner.sh
opt/bbmap-39.76-0/xdrophaligner.sh
opt/bbmap-39.76-0/zz_rename_package.sh
share/bbmap/resources/16S_15mers.fa
share/bbmap/resources/16S_consensus_sequence.fa
share/bbmap/resources/18S_15mers.fa
share/bbmap/resources/18S_consensus_sequence.fa
share/bbmap/resources/23S_15mers.fa
share/bbmap/resources/23S_consensus_sequence.fa
share/bbmap/resources/5S_10mers.fa
share/bbmap/resources/5S_11mers.fa
share/bbmap/resources/5S_12mers.fa
share/bbmap/resources/5S_15mers.fa
share/bbmap/resources/5S_9mers.fa
share/bbmap/resources/5S_consensus_sequence.fa
share/bbmap/resources/Covid19_ref.fa
share/bbmap/resources/ITS_animal_consensus_sequence.fq
share/bbmap/resources/ITS_consensus_sequence.fq
share/bbmap/resources/ITS_fungi_consensus_sequence.fq
share/bbmap/resources/ITS_nonfungi_consensus_sequence.fq
share/bbmap/resources/ITS_other_consensus_sequence.fq
share/bbmap/resources/ITS_plant_consensus_sequence.fq
share/bbmap/resources/ITS_universal_consensus_sequence.fq
share/bbmap/resources/PacBioAdapter.fa
share/bbmap/resources/SIP_spikeins.fa.gz
share/bbmap/resources/adapters.fa
share/bbmap/resources/adapters_no_transposase.fa.gz
share/bbmap/resources/artic3.fasta
share/bbmap/resources/bbmerge.bbnet
share/bbmap/resources/blacklist_nt_merged.sketch
share/bbmap/resources/blacklist_prokprot_merged.sketch
share/bbmap/resources/blacklist_refseq_merged.sketch
share/bbmap/resources/blacklist_silva_merged.sketch
share/bbmap/resources/contents.txt
share/bbmap/resources/crelox.fa.gz
share/bbmap/resources/crispr.bbnet.gz
share/bbmap/resources/crisprs.fa.gz
share/bbmap/resources/entropy_k4_w150.tsv
share/bbmap/resources/favicon.ico
share/bbmap/resources/kapatags.L40.fa
share/bbmap/resources/lambda.fa.gz
share/bbmap/resources/lfpe.linker.fa.gz
share/bbmap/resources/lsu_15mers.fa
share/bbmap/resources/m16S_consensus_sequence.fa
share/bbmap/resources/m18S_consensus_sequence.fa
share/bbmap/resources/minorAlleleCount.txt
share/bbmap/resources/model.pgm
share/bbmap/resources/mtst.fa
share/bbmap/resources/nextera.fa.gz
share/bbmap/resources/nextera_LMP_adapter.fa.gz
share/bbmap/resources/nextera_LMP_linker.fa.gz
share/bbmap/resources/p16S_consensus_sequence.fa
share/bbmap/resources/pJET1.2.fa
share/bbmap/resources/phix174_ill.ref.fa.gz
share/bbmap/resources/phix2.fa.gz
share/bbmap/resources/phix_adapters.fa
share/bbmap/resources/phix_adapters.fa.gz
share/bbmap/resources/polyA.fa.gz
share/bbmap/resources/polya.fa
share/bbmap/resources/polyc.fa
share/bbmap/resources/polyg.fa
share/bbmap/resources/polyt.fa
share/bbmap/resources/primes.txt.gz
share/bbmap/resources/quickbin1D_all.bbnet
share/bbmap/resources/quickbinND_all.bbnet
share/bbmap/resources/remote_files.txt
share/bbmap/resources/remote_files_old.txt
share/bbmap/resources/sample1.fq.gz
share/bbmap/resources/sample2.fq.gz
share/bbmap/resources/sequencing_artifacts.fa.gz
share/bbmap/resources/short.fa
share/bbmap/resources/shred4merFractions.tsv
share/bbmap/resources/ssu_15mers.fa
share/bbmap/resources/tRNA_10mers.fa
share/bbmap/resources/tRNA_11mers.fa
share/bbmap/resources/tRNA_15mers.fa
share/bbmap/resources/tRNA_16mers.fa
share/bbmap/resources/tRNA_consensus_sequence.fa
share/bbmap/resources/tax_server.html
share/bbmap/resources/truseq.fa.gz
share/bbmap/resources/truseq_rna.fa.gz
