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/ddlcalibrate.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/lowcomplexcalibrate.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/testalignersbatch.sh
bin/testalignerslength.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-39.81-1/README.md
opt/bbmap-39.81-1/a_sample_mt.sh
opt/bbmap-39.81-1/addadapters.sh
opt/bbmap-39.81-1/addssu.sh
opt/bbmap-39.81-1/adjusthomopolymers.sh
opt/bbmap-39.81-1/alignrandom.sh
opt/bbmap-39.81-1/alltoall.sh
opt/bbmap-39.81-1/analyzeaccession.sh
opt/bbmap-39.81-1/analyzegenes.sh
opt/bbmap-39.81-1/analyzesketchresults.sh
opt/bbmap-39.81-1/applyvariants.sh
opt/bbmap-39.81-1/bamlinestreamer.sh
opt/bbmap-39.81-1/bandedaligner.sh
opt/bbmap-39.81-1/bandedplusaligner.sh
opt/bbmap-39.81-1/bbcms.sh
opt/bbmap-39.81-1/bbcountunique.sh
opt/bbmap-39.81-1/bbcrisprfinder.sh
opt/bbmap-39.81-1/bbduk.sh
opt/bbmap-39.81-1/bbdukOld.sh
opt/bbmap-39.81-1/bbdukS.sh
opt/bbmap-39.81-1/bbest.sh
opt/bbmap-39.81-1/bbfakereads.sh
opt/bbmap-39.81-1/bbmap.sh
opt/bbmap-39.81-1/bbmapskimmer.sh
opt/bbmap-39.81-1/bbmask.sh
opt/bbmap-39.81-1/bbmerge-auto.sh
opt/bbmap-39.81-1/bbmerge.sh
opt/bbmap-39.81-1/bbnorm.sh
opt/bbmap-39.81-1/bbrealign.sh
opt/bbmap-39.81-1/bbrename.sh
opt/bbmap-39.81-1/bbsketch.sh
opt/bbmap-39.81-1/bbsort.sh
opt/bbmap-39.81-1/bbsplit.sh
opt/bbmap-39.81-1/bbsplitpairs.sh
opt/bbmap-39.81-1/bbstats.sh
opt/bbmap-39.81-1/bbtools.jar
opt/bbmap-39.81-1/bbversion.sh
opt/bbmap-39.81-1/bbwrap.sh
opt/bbmap-39.81-1/bitbucket-pipelines.yml
opt/bbmap-39.81-1/bloomfilter.sh
opt/bbmap-39.81-1/bloomfilterparser.sh
opt/bbmap-39.81-1/build.xml
opt/bbmap-39.81-1/build_env_setup.sh
opt/bbmap-39.81-1/calcmem.sh
opt/bbmap-39.81-1/calctruequality.sh
opt/bbmap-39.81-1/callgenes.sh
opt/bbmap-39.81-1/callpeaks.sh
opt/bbmap-39.81-1/callvariants.sh
opt/bbmap-39.81-1/callvariants2.sh
opt/bbmap-39.81-1/cat.sh
opt/bbmap-39.81-1/cbcl2text.sh
opt/bbmap-39.81-1/cg2illumina.sh
opt/bbmap-39.81-1/checkstrand.sh
opt/bbmap-39.81-1/cladeloader.sh
opt/bbmap-39.81-1/cladeserver.sh
opt/bbmap-39.81-1/cloudplot.sh
opt/bbmap-39.81-1/clumpify.sh
opt/bbmap-39.81-1/commonkmers.sh
opt/bbmap-39.81-1/comparegff.sh
opt/bbmap-39.81-1/comparelabels.sh
opt/bbmap-39.81-1/comparesketch.sh
opt/bbmap-39.81-1/comparessu.sh
opt/bbmap-39.81-1/comparevcf.sh
opt/bbmap-39.81-1/conda_build.sh
opt/bbmap-39.81-1/config/cluster16s.txt
opt/bbmap-39.81-1/config/filter16s.txt
opt/bbmap-39.81-1/config/histograms.txt
opt/bbmap-39.81-1/config/recalibrate.txt
opt/bbmap-39.81-1/config/rnaseq.txt
opt/bbmap-39.81-1/config/trimadapters.txt
opt/bbmap-39.81-1/consect.sh
opt/bbmap-39.81-1/consensus.sh
opt/bbmap-39.81-1/copyfile.sh
opt/bbmap-39.81-1/countbarcodes.sh
opt/bbmap-39.81-1/countbarcodes2.sh
opt/bbmap-39.81-1/countduplicates.sh
opt/bbmap-39.81-1/countgc.sh
opt/bbmap-39.81-1/countsharedlines.sh
opt/bbmap-39.81-1/covmaker.sh
opt/bbmap-39.81-1/crossblock.sh
opt/bbmap-39.81-1/crosscontaminate.sh
opt/bbmap-39.81-1/crosscutaligner.sh
opt/bbmap-39.81-1/cutgff.sh
opt/bbmap-39.81-1/cutprimers.sh
opt/bbmap-39.81-1/ddlcalibrate.sh
opt/bbmap-39.81-1/decontaminate.sh
opt/bbmap-39.81-1/dedupe.sh
opt/bbmap-39.81-1/dedupe2.sh
opt/bbmap-39.81-1/dedupebymapping.sh
opt/bbmap-39.81-1/demuxbyname.sh
opt/bbmap-39.81-1/demuxserver.sh
opt/bbmap-39.81-1/diskbench.sh
opt/bbmap-39.81-1/docs/BBTools_List.txt
opt/bbmap-39.81-1/docs/Legal.txt
opt/bbmap-39.81-1/docs/Legal_Illumina.txt
opt/bbmap-39.81-1/docs/RestartingServers.txt
opt/bbmap-39.81-1/docs/TableOfContents.txt
opt/bbmap-39.81-1/docs/ToolDescriptions.txt
opt/bbmap-39.81-1/docs/UsageGuide.txt
opt/bbmap-39.81-1/docs/bbcms.txt
opt/bbmap-39.81-1/docs/changelog.txt
opt/bbmap-39.81-1/docs/citation.txt
opt/bbmap-39.81-1/docs/compiling.txt
opt/bbmap-39.81-1/docs/git.txt
opt/bbmap-39.81-1/docs/guides/A_SampleGuide.txt
opt/bbmap-39.81-1/docs/guides/AddAdaptersGuide.txt
opt/bbmap-39.81-1/docs/guides/BBDukGuide.txt
opt/bbmap-39.81-1/docs/guides/BBMapGuide.txt
opt/bbmap-39.81-1/docs/guides/BBMap_old_readme.txt
opt/bbmap-39.81-1/docs/guides/BBMaskGuide.txt
opt/bbmap-39.81-1/docs/guides/BBMergeGuide.txt
opt/bbmap-39.81-1/docs/guides/BBNormGuide.txt
opt/bbmap-39.81-1/docs/guides/BBSketchGuide.txt
opt/bbmap-39.81-1/docs/guides/CalcUniquenessGuide.txt
opt/bbmap-39.81-1/docs/guides/CallVariantsGuide.txt
opt/bbmap-39.81-1/docs/guides/ClumpifyGuide.txt
opt/bbmap-39.81-1/docs/guides/DedupeGuide.txt
opt/bbmap-39.81-1/docs/guides/FilterByTileGuide.txt
opt/bbmap-39.81-1/docs/guides/PreprocessingGuide.txt
opt/bbmap-39.81-1/docs/guides/ReformatGuide.txt
opt/bbmap-39.81-1/docs/guides/RepairGuide.txt
opt/bbmap-39.81-1/docs/guides/SealGuide.txt
opt/bbmap-39.81-1/docs/guides/SplitNexteraGuide.txt
opt/bbmap-39.81-1/docs/guides/StatsGuide.txt
opt/bbmap-39.81-1/docs/guides/TadpoleGuide.txt
opt/bbmap-39.81-1/docs/guides/TaxonomyGuide.txt
opt/bbmap-39.81-1/docs/readme.txt
opt/bbmap-39.81-1/docs/readme_config.txt
opt/bbmap-39.81-1/docs/readme_filetypes.txt
opt/bbmap-39.81-1/driftingaligner.sh
opt/bbmap-39.81-1/driftingplusaligner.sh
opt/bbmap-39.81-1/estherfilter.sh
opt/bbmap-39.81-1/explodetree.sh
opt/bbmap-39.81-1/fastqscan.sh
opt/bbmap-39.81-1/fetchproks.sh
opt/bbmap-39.81-1/filescan.sh
opt/bbmap-39.81-1/filterassemblysummary.sh
opt/bbmap-39.81-1/filterbarcodes.sh
opt/bbmap-39.81-1/filterbycoverage.sh
opt/bbmap-39.81-1/filterbyname.sh
opt/bbmap-39.81-1/filterbysequence.sh
opt/bbmap-39.81-1/filterbytaxa.sh
opt/bbmap-39.81-1/filterbytile.sh
opt/bbmap-39.81-1/filterlines.sh
opt/bbmap-39.81-1/filtersam.sh
opt/bbmap-39.81-1/filtersilva.sh
opt/bbmap-39.81-1/filtersubs.sh
opt/bbmap-39.81-1/filtervcf.sh
opt/bbmap-39.81-1/findrepeats.sh
opt/bbmap-39.81-1/fix_script_paths.sh
opt/bbmap-39.81-1/fixgaps.sh
opt/bbmap-39.81-1/fungalrelease.sh
opt/bbmap-39.81-1/fuse.sh
opt/bbmap-39.81-1/gbff2gff.sh
opt/bbmap-39.81-1/getreads.sh
opt/bbmap-39.81-1/gi2ancestors.sh
opt/bbmap-39.81-1/gi2taxid.sh
opt/bbmap-39.81-1/gitable.sh
opt/bbmap-39.81-1/glocalaligner.sh
opt/bbmap-39.81-1/gradebins.sh
opt/bbmap-39.81-1/grademerge.sh
opt/bbmap-39.81-1/gradesam.sh
opt/bbmap-39.81-1/icecreamfinder.sh
opt/bbmap-39.81-1/icecreamgrader.sh
opt/bbmap-39.81-1/icecreammaker.sh
opt/bbmap-39.81-1/idmatrix.sh
opt/bbmap-39.81-1/idtree.sh
opt/bbmap-39.81-1/indelfree.sh
opt/bbmap-39.81-1/invertkey.sh
opt/bbmap-39.81-1/javasetup.sh
opt/bbmap-39.81-1/jni/BBMergeOverlapper.c
opt/bbmap-39.81-1/jni/BBMergeOverlapper.o
opt/bbmap-39.81-1/jni/BandedAlignerJNI.c
opt/bbmap-39.81-1/jni/BandedAlignerJNI.o
opt/bbmap-39.81-1/jni/CMakeLists.txt
opt/bbmap-39.81-1/jni/IceCreamAlignerJNI.c
opt/bbmap-39.81-1/jni/IceCreamAlignerJNI.o
opt/bbmap-39.81-1/jni/MultiStateAligner11tsJNI.c
opt/bbmap-39.81-1/jni/MultiStateAligner11tsJNI.o
opt/bbmap-39.81-1/jni/README.txt
opt/bbmap-39.81-1/jni/align2_BandedAlignerJNI.h
opt/bbmap-39.81-1/jni/align2_MultiStateAligner11tsJNI.h
opt/bbmap-39.81-1/jni/icecream_IceCreamAlignerJNI.h
opt/bbmap-39.81-1/jni/jgi_BBMergeOverlapper.h
opt/bbmap-39.81-1/jni/libbbtoolsjni.dylib
opt/bbmap-39.81-1/jni/libbbtoolsjni.so
opt/bbmap-39.81-1/jni/makefile.linux
opt/bbmap-39.81-1/jni/makefile.osx
opt/bbmap-39.81-1/jni/run.sh
opt/bbmap-39.81-1/kapastats.sh
opt/bbmap-39.81-1/kcompress.sh
opt/bbmap-39.81-1/keepbestcopy.sh
opt/bbmap-39.81-1/khist.sh
opt/bbmap-39.81-1/kmercountexact.sh
opt/bbmap-39.81-1/kmercountmulti.sh
opt/bbmap-39.81-1/kmercountshort.sh
opt/bbmap-39.81-1/kmercoverage.sh
opt/bbmap-39.81-1/kmerfilterset.sh
opt/bbmap-39.81-1/kmerlimit.sh
opt/bbmap-39.81-1/kmerlimit2.sh
opt/bbmap-39.81-1/kmerposition.sh
opt/bbmap-39.81-1/kmutate.sh
opt/bbmap-39.81-1/license.txt
opt/bbmap-39.81-1/lilypad.sh
opt/bbmap-39.81-1/loadreads.sh
opt/bbmap-39.81-1/loglog.sh
opt/bbmap-39.81-1/lowcomplexcalibrate.sh
opt/bbmap-39.81-1/makechimeras.sh
opt/bbmap-39.81-1/makecontaminatedgenomes.sh
opt/bbmap-39.81-1/makepolymers.sh
opt/bbmap-39.81-1/makequickbinvector.sh
opt/bbmap-39.81-1/mapPacBio.sh
opt/bbmap-39.81-1/matrixtocolumns.sh
opt/bbmap-39.81-1/memdetect.sh
opt/bbmap-39.81-1/mergeOTUs.sh
opt/bbmap-39.81-1/mergebarcodes.sh
opt/bbmap-39.81-1/mergepgm.sh
opt/bbmap-39.81-1/mergeribo.sh
opt/bbmap-39.81-1/mergesam.sh
opt/bbmap-39.81-1/mergesketch.sh
opt/bbmap-39.81-1/mergesorted.sh
opt/bbmap-39.81-1/metadata_conda_debug.yaml
opt/bbmap-39.81-1/microalign.sh
opt/bbmap-39.81-1/msa.sh
opt/bbmap-39.81-1/mutate.sh
opt/bbmap-39.81-1/muxbyname.sh
opt/bbmap-39.81-1/netfilter.sh
opt/bbmap-39.81-1/novademux.sh
opt/bbmap-39.81-1/parallelogram.sh
opt/bbmap-39.81-1/partition.sh
opt/bbmap-39.81-1/phylip2fasta.sh
opt/bbmap-39.81-1/picksubset.sh
opt/bbmap-39.81-1/pileup.sh
opt/bbmap-39.81-1/pileup2.sh
opt/bbmap-39.81-1/pipelines/assembleMito_Illumina.sh
opt/bbmap-39.81-1/pipelines/assembleMito_PacBio.sh
opt/bbmap-39.81-1/pipelines/assemble_polyg_isolate_v1.sh
opt/bbmap-39.81-1/pipelines/assemble_polyg_meta_v1.sh
opt/bbmap-39.81-1/pipelines/assemblyPipeline.sh
opt/bbmap-39.81-1/pipelines/callInsertions.sh
opt/bbmap-39.81-1/pipelines/covid/makeSummary.sh
opt/bbmap-39.81-1/pipelines/covid/processCorona.sh
opt/bbmap-39.81-1/pipelines/covid/processCoronaWrapper.sh
opt/bbmap-39.81-1/pipelines/covid/readme.txt
opt/bbmap-39.81-1/pipelines/covid/recal.sh
opt/bbmap-39.81-1/pipelines/crisprPipeline.sh
opt/bbmap-39.81-1/pipelines/cutRna.sh
opt/bbmap-39.81-1/pipelines/fetch/fetchMito.sh
opt/bbmap-39.81-1/pipelines/fetch/fetchNt.sh
opt/bbmap-39.81-1/pipelines/fetch/fetchNtOuter.sh
opt/bbmap-39.81-1/pipelines/fetch/fetchPlasmid.sh
opt/bbmap-39.81-1/pipelines/fetch/fetchPlastid.sh
opt/bbmap-39.81-1/pipelines/fetch/fetchProkByGenus.sh
opt/bbmap-39.81-1/pipelines/fetch/fetchRefSeq.sh
opt/bbmap-39.81-1/pipelines/fetch/fetchRefSeqClades.sh
opt/bbmap-39.81-1/pipelines/fetch/fetchRefSeqCladesOuter.sh
opt/bbmap-39.81-1/pipelines/fetch/fetchSilva.sh
opt/bbmap-39.81-1/pipelines/fetch/fetchTaxonomy.sh
opt/bbmap-39.81-1/pipelines/fetch/runRefSeqProtein.sh
opt/bbmap-39.81-1/pipelines/fetch/sketchRefSeq.sh
opt/bbmap-39.81-1/pipelines/makeRiboKmers.sh
opt/bbmap-39.81-1/pipelines/processIMG.sh
opt/bbmap-39.81-1/pipelines/process_lane_v007.sh
opt/bbmap-39.81-1/pipelines/server/startNtServerVM.sh
opt/bbmap-39.81-1/pipelines/server/startProteinServerVM.sh
opt/bbmap-39.81-1/pipelines/server/startRefseqServerVM.sh
opt/bbmap-39.81-1/pipelines/server/startSilvaServerVM.sh
opt/bbmap-39.81-1/pipelines/server/startTaxServerVM.sh
opt/bbmap-39.81-1/pipelines/silva/fetchSilva.sh
opt/bbmap-39.81-1/pipelines/silva/make15mers.sh
opt/bbmap-39.81-1/pipelines/silva/makeCoveringSetLsu.sh
opt/bbmap-39.81-1/pipelines/silva/makeCoveringSetSsu.sh
opt/bbmap-39.81-1/pipelines/silva/makeRep.sh
opt/bbmap-39.81-1/pipelines/testPlatformQuality.sh
opt/bbmap-39.81-1/pipelines/testsketch.sh
opt/bbmap-39.81-1/pipelines/variantPipeline.sh
opt/bbmap-39.81-1/plotflowcell.sh
opt/bbmap-39.81-1/plotgc.sh
opt/bbmap-39.81-1/plothist.sh
opt/bbmap-39.81-1/plotreadposition.sh
opt/bbmap-39.81-1/polyfilter.sh
opt/bbmap-39.81-1/postfilter.sh
opt/bbmap-39.81-1/printtime.sh
opt/bbmap-39.81-1/processfrag.sh
opt/bbmap-39.81-1/processhi-c.sh
opt/bbmap-39.81-1/processspeed.sh
opt/bbmap-39.81-1/profile.sh
opt/bbmap-39.81-1/quabblealigner.sh
opt/bbmap-39.81-1/quantumaligner.sh
opt/bbmap-39.81-1/quickbin.sh
opt/bbmap-39.81-1/quickclade.sh
opt/bbmap-39.81-1/randomgenome.sh
opt/bbmap-39.81-1/randomreads.sh
opt/bbmap-39.81-1/randomreadsmg.sh
opt/bbmap-39.81-1/readlength.sh
opt/bbmap-39.81-1/reassemble.sh
opt/bbmap-39.81-1/reducecolumns.sh
opt/bbmap-39.81-1/reducesilva.sh
opt/bbmap-39.81-1/reformat.sh
opt/bbmap-39.81-1/reformat2.sh
opt/bbmap-39.81-1/reformat3.sh
opt/bbmap-39.81-1/reformatpb.sh
opt/bbmap-39.81-1/removebadbarcodes.sh
opt/bbmap-39.81-1/removecatdogmousehuman.sh
opt/bbmap-39.81-1/removehuman.sh
opt/bbmap-39.81-1/removehuman2.sh
opt/bbmap-39.81-1/removemicrobes.sh
opt/bbmap-39.81-1/removesmartbell.sh
opt/bbmap-39.81-1/rename.sh
opt/bbmap-39.81-1/renamebymapping.sh
opt/bbmap-39.81-1/renamebysketch.sh
opt/bbmap-39.81-1/renameimg.sh
opt/bbmap-39.81-1/renameref.sh
opt/bbmap-39.81-1/repair.sh
opt/bbmap-39.81-1/replaceheaders.sh
opt/bbmap-39.81-1/representative.sh
opt/bbmap-39.81-1/resources/16S_15mers.fa
opt/bbmap-39.81-1/resources/16S_consensus_sequence.fa
opt/bbmap-39.81-1/resources/18S_15mers.fa
opt/bbmap-39.81-1/resources/18S_consensus_sequence.fa
opt/bbmap-39.81-1/resources/23S_15mers.fa
opt/bbmap-39.81-1/resources/23S_consensus_sequence.fa
opt/bbmap-39.81-1/resources/5S_10mers.fa
opt/bbmap-39.81-1/resources/5S_11mers.fa
opt/bbmap-39.81-1/resources/5S_12mers.fa
opt/bbmap-39.81-1/resources/5S_15mers.fa
opt/bbmap-39.81-1/resources/5S_9mers.fa
opt/bbmap-39.81-1/resources/5S_consensus_sequence.fa
opt/bbmap-39.81-1/resources/Covid19_ref.fa
opt/bbmap-39.81-1/resources/ITS_animal_consensus_sequence.fq
opt/bbmap-39.81-1/resources/ITS_consensus_sequence.fq
opt/bbmap-39.81-1/resources/ITS_fungi_consensus_sequence.fq
opt/bbmap-39.81-1/resources/ITS_nonfungi_consensus_sequence.fq
opt/bbmap-39.81-1/resources/ITS_other_consensus_sequence.fq
opt/bbmap-39.81-1/resources/ITS_plant_consensus_sequence.fq
opt/bbmap-39.81-1/resources/ITS_universal_consensus_sequence.fq
opt/bbmap-39.81-1/resources/PacBioAdapter.fa
opt/bbmap-39.81-1/resources/SIP_spikeins.fa.gz
opt/bbmap-39.81-1/resources/adapters.fa
opt/bbmap-39.81-1/resources/adapters_no_transposase.fa.gz
opt/bbmap-39.81-1/resources/artic3.fasta
opt/bbmap-39.81-1/resources/bbmerge.bbnet
opt/bbmap-39.81-1/resources/blacklist_nt_merged.sketch
opt/bbmap-39.81-1/resources/blacklist_prokprot_merged.sketch
opt/bbmap-39.81-1/resources/blacklist_refseq_merged.sketch
opt/bbmap-39.81-1/resources/blacklist_silva_merged.sketch
opt/bbmap-39.81-1/resources/cardinalityCorrectionDDL.tsv.gz
opt/bbmap-39.81-1/resources/cardinalityCorrectionDDL8.tsv.gz
opt/bbmap-39.81-1/resources/cardinalityCorrectionDLL3.tsv.gz
opt/bbmap-39.81-1/resources/cardinalityCorrectionDLL3v2.tsv.gz
opt/bbmap-39.81-1/resources/cardinalityCorrectionDLL4.tsv.gz
opt/bbmap-39.81-1/resources/cardinalityCorrectionLL6.tsv.gz
opt/bbmap-39.81-1/resources/cardinalityCorrectionPLL16c.tsv.gz
opt/bbmap-39.81-1/resources/cardinalityCorrectionULL8-ACT.tsv.gz
opt/bbmap-39.81-1/resources/cardinalityCorrectionULL8-FRZ.tsv.gz
opt/bbmap-39.81-1/resources/cardinalityCorrectionULL8.tsv.gz
opt/bbmap-39.81-1/resources/contents.txt
opt/bbmap-39.81-1/resources/crelox.fa.gz
opt/bbmap-39.81-1/resources/crispr.bbnet.gz
opt/bbmap-39.81-1/resources/crisprs.fa.gz
opt/bbmap-39.81-1/resources/entropy_k4_w150.tsv
opt/bbmap-39.81-1/resources/favicon.ico
opt/bbmap-39.81-1/resources/kapatags.L40.fa
opt/bbmap-39.81-1/resources/lambda.fa.gz
opt/bbmap-39.81-1/resources/lfpe.linker.fa.gz
opt/bbmap-39.81-1/resources/lsu_15mers.fa
opt/bbmap-39.81-1/resources/m16S_consensus_sequence.fa
opt/bbmap-39.81-1/resources/m18S_consensus_sequence.fa
opt/bbmap-39.81-1/resources/minorAlleleCount.txt
opt/bbmap-39.81-1/resources/model.pgm
opt/bbmap-39.81-1/resources/mtst.fa
opt/bbmap-39.81-1/resources/nextera.fa.gz
opt/bbmap-39.81-1/resources/nextera_LMP_adapter.fa.gz
opt/bbmap-39.81-1/resources/nextera_LMP_linker.fa.gz
opt/bbmap-39.81-1/resources/p16S_consensus_sequence.fa
opt/bbmap-39.81-1/resources/pJET1.2.fa
opt/bbmap-39.81-1/resources/phix174_ill.ref.fa.gz
opt/bbmap-39.81-1/resources/phix2.fa.gz
opt/bbmap-39.81-1/resources/phix_adapters.fa
opt/bbmap-39.81-1/resources/phix_adapters.fa.gz
opt/bbmap-39.81-1/resources/polyA.fa.gz
opt/bbmap-39.81-1/resources/polya.fa
opt/bbmap-39.81-1/resources/polyc.fa
opt/bbmap-39.81-1/resources/polyg.fa
opt/bbmap-39.81-1/resources/polyt.fa
opt/bbmap-39.81-1/resources/primes.txt.gz
opt/bbmap-39.81-1/resources/quickbin1D_all.bbnet
opt/bbmap-39.81-1/resources/quickbinND_all.bbnet
opt/bbmap-39.81-1/resources/remote_files.txt
opt/bbmap-39.81-1/resources/remote_files_old.txt
opt/bbmap-39.81-1/resources/sample1.fq.gz
opt/bbmap-39.81-1/resources/sample2.fq.gz
opt/bbmap-39.81-1/resources/sequencing_artifacts.fa.gz
opt/bbmap-39.81-1/resources/short.fa
opt/bbmap-39.81-1/resources/shred4merFractions.tsv
opt/bbmap-39.81-1/resources/ssu_15mers.fa
opt/bbmap-39.81-1/resources/tRNA_10mers.fa
opt/bbmap-39.81-1/resources/tRNA_11mers.fa
opt/bbmap-39.81-1/resources/tRNA_15mers.fa
opt/bbmap-39.81-1/resources/tRNA_16mers.fa
opt/bbmap-39.81-1/resources/tRNA_consensus_sequence.fa
opt/bbmap-39.81-1/resources/tax_server.html
opt/bbmap-39.81-1/resources/tree.taxtree.gz
opt/bbmap-39.81-1/resources/truseq.fa.gz
opt/bbmap-39.81-1/resources/truseq_rna.fa.gz
opt/bbmap-39.81-1/rqcfilter.sh
opt/bbmap-39.81-1/rqcfilter2.sh
opt/bbmap-39.81-1/rqcfilter3.sh
opt/bbmap-39.81-1/runhmm.sh
opt/bbmap-39.81-1/samstreamer.sh
opt/bbmap-39.81-1/samtoroc.sh
opt/bbmap-39.81-1/scalarintervals.sh
opt/bbmap-39.81-1/scalars.sh
opt/bbmap-39.81-1/scoresequence.sh
opt/bbmap-39.81-1/scrabblealigner.sh
opt/bbmap-39.81-1/seal.sh
opt/bbmap-39.81-1/sendclade.sh
opt/bbmap-39.81-1/sendsketch.sh
opt/bbmap-39.81-1/seqtovec.sh
opt/bbmap-39.81-1/shred.sh
opt/bbmap-39.81-1/shrinkaccession.sh
opt/bbmap-39.81-1/shuffle.sh
opt/bbmap-39.81-1/shuffle2.sh
opt/bbmap-39.81-1/sketch.sh
opt/bbmap-39.81-1/sketchblacklist.sh
opt/bbmap-39.81-1/sketchblacklist2.sh
opt/bbmap-39.81-1/smithwaterman.sh
opt/bbmap-39.81-1/sortbyname.sh
opt/bbmap-39.81-1/splitbytaxa.sh
opt/bbmap-39.81-1/splitnextera.sh
opt/bbmap-39.81-1/splitribo.sh
opt/bbmap-39.81-1/splitsam.sh
opt/bbmap-39.81-1/splitsam4way.sh
opt/bbmap-39.81-1/splitsam6way.sh
opt/bbmap-39.81-1/stats.sh
opt/bbmap-39.81-1/stats3.sh
opt/bbmap-39.81-1/statswrapper.sh
opt/bbmap-39.81-1/stream.sh
opt/bbmap-39.81-1/streamsam.sh
opt/bbmap-39.81-1/subsketch.sh
opt/bbmap-39.81-1/summarizecontam.sh
opt/bbmap-39.81-1/summarizecoverage.sh
opt/bbmap-39.81-1/summarizecrossblock.sh
opt/bbmap-39.81-1/summarizemerge.sh
opt/bbmap-39.81-1/summarizequast.sh
opt/bbmap-39.81-1/summarizescafstats.sh
opt/bbmap-39.81-1/summarizeseal.sh
opt/bbmap-39.81-1/summarizesketch.sh
opt/bbmap-39.81-1/synthmda.sh
opt/bbmap-39.81-1/tadpipe.sh
opt/bbmap-39.81-1/tadpole.sh
opt/bbmap-39.81-1/tadwrapper.sh
opt/bbmap-39.81-1/tagandmerge.sh
opt/bbmap-39.81-1/taxonomy.sh
opt/bbmap-39.81-1/taxserver.sh
opt/bbmap-39.81-1/taxsize.sh
opt/bbmap-39.81-1/taxtree.sh
opt/bbmap-39.81-1/testaligners.sh
opt/bbmap-39.81-1/testaligners2.sh
opt/bbmap-39.81-1/testalignersbatch.sh
opt/bbmap-39.81-1/testalignerslength.sh
opt/bbmap-39.81-1/testfilesystem.sh
opt/bbmap-39.81-1/testformat.sh
opt/bbmap-39.81-1/testformat2.sh
opt/bbmap-39.81-1/tetramerfreq.sh
opt/bbmap-39.81-1/textfile.sh
opt/bbmap-39.81-1/tiledump.sh
opt/bbmap-39.81-1/train.sh
opt/bbmap-39.81-1/translate6frames.sh
opt/bbmap-39.81-1/trimcontigs.sh
opt/bbmap-39.81-1/unicode2ascii.sh
opt/bbmap-39.81-1/unzip.sh
opt/bbmap-39.81-1/vcf2gff.sh
opt/bbmap-39.81-1/visualizealignment.sh
opt/bbmap-39.81-1/wavefrontaligner.sh
opt/bbmap-39.81-1/wavefrontalignerviz.sh
opt/bbmap-39.81-1/webcheck.sh
opt/bbmap-39.81-1/wobblealigner.sh
opt/bbmap-39.81-1/wobbleplusaligner.sh
opt/bbmap-39.81-1/xdrophaligner.sh
opt/bbmap-39.81-1/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/cardinalityCorrectionDDL.tsv.gz
share/bbmap/resources/cardinalityCorrectionDDL8.tsv.gz
share/bbmap/resources/cardinalityCorrectionDLL3.tsv.gz
share/bbmap/resources/cardinalityCorrectionDLL3v2.tsv.gz
share/bbmap/resources/cardinalityCorrectionDLL4.tsv.gz
share/bbmap/resources/cardinalityCorrectionLL6.tsv.gz
share/bbmap/resources/cardinalityCorrectionPLL16c.tsv.gz
share/bbmap/resources/cardinalityCorrectionULL8-ACT.tsv.gz
share/bbmap/resources/cardinalityCorrectionULL8-FRZ.tsv.gz
share/bbmap/resources/cardinalityCorrectionULL8.tsv.gz
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/tree.taxtree.gz
share/bbmap/resources/truseq.fa.gz
share/bbmap/resources/truseq_rna.fa.gz
