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| 1 | +docker: quay.io/biocontainers/bbmap |
| 2 | +url: https://quay.io/repository/biocontainers/bbmap |
| 3 | +maintainer: '@marcodelapierre' |
| 4 | +description: 'BBMap is a short read aligner, as well as various other bioinformatic tools.' |
| 5 | +latest: |
| 6 | + 38.91--he522d1c_1: sha256:5679f2c146844662be023769146fa787ea101f3dd833ade36aaa0bb533c9939a |
| 7 | +tags: |
| 8 | + 38.89--h1296035_0: sha256:acc26b0e54b1323c2db287fabb8bffecda94e766b6759dfdddc7472687b52f33 |
| 9 | + 38.90--he522d1c_3: sha256:e85733071f68bc84959aa97155f9d13b87fdfd17f41703fe861c057a56dec2b0 |
| 10 | + 38.91--he522d1c_1: sha256:5679f2c146844662be023769146fa787ea101f3dd833ade36aaa0bb533c9939a |
| 11 | +aliases: |
| 12 | + a_sample_mt.sh: /usr/local/bin/a_sample_mt.sh |
| 13 | + addadapters.sh: /usr/local/bin/addadapters.sh |
| 14 | + addssu.sh: /usr/local/bin/addssu.sh |
| 15 | + adjusthomopolymers.sh: /usr/local/bin/adjusthomopolymers.sh |
| 16 | + alltoall.sh: /usr/local/bin/alltoall.sh |
| 17 | + analyzeaccession.sh: /usr/local/bin/analyzeaccession.sh |
| 18 | + analyzegenes.sh: /usr/local/bin/analyzegenes.sh |
| 19 | + analyzesketchresults.sh: /usr/local/bin/analyzesketchresults.sh |
| 20 | + applyvariants.sh: /usr/local/bin/applyvariants.sh |
| 21 | + bbcms.sh: /usr/local/bin/bbcms.sh |
| 22 | + bbcountunique.sh: /usr/local/bin/bbcountunique.sh |
| 23 | + bbduk.sh: /usr/local/bin/bbduk.sh |
| 24 | + bbest.sh: /usr/local/bin/bbest.sh |
| 25 | + bbfakereads.sh: /usr/local/bin/bbfakereads.sh |
| 26 | + bbmap.sh: /usr/local/bin/bbmap.sh |
| 27 | + bbmapskimmer.sh: /usr/local/bin/bbmapskimmer.sh |
| 28 | + bbmask.sh: /usr/local/bin/bbmask.sh |
| 29 | + bbmerge-auto.sh: /usr/local/bin/bbmerge-auto.sh |
| 30 | + bbmerge.sh: /usr/local/bin/bbmerge.sh |
| 31 | + bbnorm.sh: /usr/local/bin/bbnorm.sh |
| 32 | + bbrealign.sh: /usr/local/bin/bbrealign.sh |
| 33 | + bbrename.sh: /usr/local/bin/bbrename.sh |
| 34 | + bbsketch.sh: /usr/local/bin/bbsketch.sh |
| 35 | + bbsplit.sh: /usr/local/bin/bbsplit.sh |
| 36 | + bbsplitpairs.sh: /usr/local/bin/bbsplitpairs.sh |
| 37 | + bbstats.sh: /usr/local/bin/bbstats.sh |
| 38 | + bbversion.sh: /usr/local/bin/bbversion.sh |
| 39 | + bbwrap.sh: /usr/local/bin/bbwrap.sh |
| 40 | + bloomfilter.sh: /usr/local/bin/bloomfilter.sh |
| 41 | + build_env_setup.sh: /usr/local/bin/build_env_setup.sh |
| 42 | + calcmem.sh: /usr/local/bin/calcmem.sh |
| 43 | + calctruequality.sh: /usr/local/bin/calctruequality.sh |
| 44 | + callgenes.sh: /usr/local/bin/callgenes.sh |
| 45 | + callpeaks.sh: /usr/local/bin/callpeaks.sh |
| 46 | + callvariants.sh: /usr/local/bin/callvariants.sh |
| 47 | + callvariants2.sh: /usr/local/bin/callvariants2.sh |
| 48 | + clumpify.sh: /usr/local/bin/clumpify.sh |
| 49 | + commonkmers.sh: /usr/local/bin/commonkmers.sh |
| 50 | + comparegff.sh: /usr/local/bin/comparegff.sh |
| 51 | + comparesketch.sh: /usr/local/bin/comparesketch.sh |
| 52 | + comparessu.sh: /usr/local/bin/comparessu.sh |
| 53 | + comparevcf.sh: /usr/local/bin/comparevcf.sh |
| 54 | + conda_build.sh: /usr/local/bin/conda_build.sh |
| 55 | + consect.sh: /usr/local/bin/consect.sh |
| 56 | + consensus.sh: /usr/local/bin/consensus.sh |
| 57 | + countbarcodes.sh: /usr/local/bin/countbarcodes.sh |
| 58 | + countgc.sh: /usr/local/bin/countgc.sh |
| 59 | + countsharedlines.sh: /usr/local/bin/countsharedlines.sh |
| 60 | + crossblock.sh: /usr/local/bin/crossblock.sh |
| 61 | + crosscontaminate.sh: /usr/local/bin/crosscontaminate.sh |
| 62 | + cutgff.sh: /usr/local/bin/cutgff.sh |
| 63 | + cutprimers.sh: /usr/local/bin/cutprimers.sh |
| 64 | + decontaminate.sh: /usr/local/bin/decontaminate.sh |
| 65 | + dedupe.sh: /usr/local/bin/dedupe.sh |
| 66 | + dedupe2.sh: /usr/local/bin/dedupe2.sh |
| 67 | + dedupebymapping.sh: /usr/local/bin/dedupebymapping.sh |
| 68 | + demuxbyname.sh: /usr/local/bin/demuxbyname.sh |
| 69 | + diskbench.sh: /usr/local/bin/diskbench.sh |
| 70 | + estherfilter.sh: /usr/local/bin/estherfilter.sh |
| 71 | + explodetree.sh: /usr/local/bin/explodetree.sh |
| 72 | + fetchproks.sh: /usr/local/bin/fetchproks.sh |
| 73 | + filterassemblysummary.sh: /usr/local/bin/filterassemblysummary.sh |
| 74 | + filterbarcodes.sh: /usr/local/bin/filterbarcodes.sh |
| 75 | + filterbycoverage.sh: /usr/local/bin/filterbycoverage.sh |
| 76 | + filterbyname.sh: /usr/local/bin/filterbyname.sh |
| 77 | + filterbysequence.sh: /usr/local/bin/filterbysequence.sh |
| 78 | + filterbytaxa.sh: /usr/local/bin/filterbytaxa.sh |
| 79 | + filterbytile.sh: /usr/local/bin/filterbytile.sh |
| 80 | + filterlines.sh: /usr/local/bin/filterlines.sh |
| 81 | + filterqc.sh: /usr/local/bin/filterqc.sh |
| 82 | + filtersam.sh: /usr/local/bin/filtersam.sh |
| 83 | + filtersilva.sh: /usr/local/bin/filtersilva.sh |
| 84 | + filtersubs.sh: /usr/local/bin/filtersubs.sh |
| 85 | + filtervcf.sh: /usr/local/bin/filtervcf.sh |
| 86 | + fixgaps.sh: /usr/local/bin/fixgaps.sh |
| 87 | + fungalrelease.sh: /usr/local/bin/fungalrelease.sh |
| 88 | + fuse.sh: /usr/local/bin/fuse.sh |
| 89 | + gbff2gff.sh: /usr/local/bin/gbff2gff.sh |
| 90 | + getreads.sh: /usr/local/bin/getreads.sh |
| 91 | + gi2ancestors.sh: /usr/local/bin/gi2ancestors.sh |
| 92 | + gi2taxid.sh: /usr/local/bin/gi2taxid.sh |
| 93 | + gitable.sh: /usr/local/bin/gitable.sh |
| 94 | + grademerge.sh: /usr/local/bin/grademerge.sh |
| 95 | + gradesam.sh: /usr/local/bin/gradesam.sh |
| 96 | + icecreamfinder.sh: /usr/local/bin/icecreamfinder.sh |
| 97 | + icecreamgrader.sh: /usr/local/bin/icecreamgrader.sh |
| 98 | + icecreammaker.sh: /usr/local/bin/icecreammaker.sh |
| 99 | + idmatrix.sh: /usr/local/bin/idmatrix.sh |
| 100 | + idtree.sh: /usr/local/bin/idtree.sh |
| 101 | + invertkey.sh: /usr/local/bin/invertkey.sh |
| 102 | + kapastats.sh: /usr/local/bin/kapastats.sh |
| 103 | + kcompress.sh: /usr/local/bin/kcompress.sh |
| 104 | + keepbestcopy.sh: /usr/local/bin/keepbestcopy.sh |
| 105 | + khist.sh: /usr/local/bin/khist.sh |
| 106 | + kmercountexact.sh: /usr/local/bin/kmercountexact.sh |
| 107 | + kmercountmulti.sh: /usr/local/bin/kmercountmulti.sh |
| 108 | + kmercoverage.sh: /usr/local/bin/kmercoverage.sh |
| 109 | + kmerfilterset.sh: /usr/local/bin/kmerfilterset.sh |
| 110 | + kmerlimit.sh: /usr/local/bin/kmerlimit.sh |
| 111 | + kmerlimit2.sh: /usr/local/bin/kmerlimit2.sh |
| 112 | + kmerposition.sh: /usr/local/bin/kmerposition.sh |
| 113 | + kmutate.sh: /usr/local/bin/kmutate.sh |
| 114 | + lilypad.sh: /usr/local/bin/lilypad.sh |
| 115 | + loadreads.sh: /usr/local/bin/loadreads.sh |
| 116 | + loglog.sh: /usr/local/bin/loglog.sh |
| 117 | + makechimeras.sh: /usr/local/bin/makechimeras.sh |
| 118 | + makecontaminatedgenomes.sh: /usr/local/bin/makecontaminatedgenomes.sh |
| 119 | + makepolymers.sh: /usr/local/bin/makepolymers.sh |
| 120 | + mapPacBio.sh: /usr/local/bin/mapPacBio.sh |
| 121 | + matrixtocolumns.sh: /usr/local/bin/matrixtocolumns.sh |
| 122 | + mergeOTUs.sh: /usr/local/bin/mergeOTUs.sh |
| 123 | + mergebarcodes.sh: /usr/local/bin/mergebarcodes.sh |
| 124 | + mergepgm.sh: /usr/local/bin/mergepgm.sh |
| 125 | + mergeribo.sh: /usr/local/bin/mergeribo.sh |
| 126 | + mergesam.sh: /usr/local/bin/mergesam.sh |
| 127 | + mergesketch.sh: /usr/local/bin/mergesketch.sh |
| 128 | + mergesorted.sh: /usr/local/bin/mergesorted.sh |
| 129 | + msa.sh: /usr/local/bin/msa.sh |
| 130 | + mutate.sh: /usr/local/bin/mutate.sh |
| 131 | + muxbyname.sh: /usr/local/bin/muxbyname.sh |
| 132 | + partition.sh: /usr/local/bin/partition.sh |
| 133 | + phylip2fasta.sh: /usr/local/bin/phylip2fasta.sh |
| 134 | + pileup.sh: /usr/local/bin/pileup.sh |
| 135 | + plotflowcell.sh: /usr/local/bin/plotflowcell.sh |
| 136 | + plotgc.sh: /usr/local/bin/plotgc.sh |
| 137 | + postfilter.sh: /usr/local/bin/postfilter.sh |
| 138 | + printtime.sh: /usr/local/bin/printtime.sh |
| 139 | + processfrag.sh: /usr/local/bin/processfrag.sh |
| 140 | + processhi-c.sh: /usr/local/bin/processhi-c.sh |
| 141 | + processspeed.sh: /usr/local/bin/processspeed.sh |
| 142 | + randomgenome.sh: /usr/local/bin/randomgenome.sh |
| 143 | + randomreads.sh: /usr/local/bin/randomreads.sh |
| 144 | + readlength.sh: /usr/local/bin/readlength.sh |
| 145 | + readqc.sh: /usr/local/bin/readqc.sh |
| 146 | + reducesilva.sh: /usr/local/bin/reducesilva.sh |
| 147 | + reformat.sh: /usr/local/bin/reformat.sh |
| 148 | + reformatpb.sh: /usr/local/bin/reformatpb.sh |
| 149 | + removebadbarcodes.sh: /usr/local/bin/removebadbarcodes.sh |
| 150 | + removecatdogmousehuman.sh: /usr/local/bin/removecatdogmousehuman.sh |
| 151 | + removehuman.sh: /usr/local/bin/removehuman.sh |
| 152 | + removehuman2.sh: /usr/local/bin/removehuman2.sh |
| 153 | + removemicrobes.sh: /usr/local/bin/removemicrobes.sh |
| 154 | + removesmartbell.sh: /usr/local/bin/removesmartbell.sh |
| 155 | + rename.sh: /usr/local/bin/rename.sh |
| 156 | + renameimg.sh: /usr/local/bin/renameimg.sh |
| 157 | + repair.sh: /usr/local/bin/repair.sh |
| 158 | + replaceheaders.sh: /usr/local/bin/replaceheaders.sh |
| 159 | + representative.sh: /usr/local/bin/representative.sh |
| 160 | + rqcfilter.sh: /usr/local/bin/rqcfilter.sh |
| 161 | + rqcfilter2.sh: /usr/local/bin/rqcfilter2.sh |
| 162 | + runhmm.sh: /usr/local/bin/runhmm.sh |
| 163 | + samtoroc.sh: /usr/local/bin/samtoroc.sh |
| 164 | + seal.sh: /usr/local/bin/seal.sh |
| 165 | + sendsketch.sh: /usr/local/bin/sendsketch.sh |
| 166 | + shred.sh: /usr/local/bin/shred.sh |
| 167 | + shrinkaccession.sh: /usr/local/bin/shrinkaccession.sh |
| 168 | + shuffle.sh: /usr/local/bin/shuffle.sh |
| 169 | + shuffle2.sh: /usr/local/bin/shuffle2.sh |
| 170 | + sketch.sh: /usr/local/bin/sketch.sh |
| 171 | + sketchblacklist.sh: /usr/local/bin/sketchblacklist.sh |
| 172 | + sketchblacklist2.sh: /usr/local/bin/sketchblacklist2.sh |
| 173 | + sortbyname.sh: /usr/local/bin/sortbyname.sh |
| 174 | + splitbytaxa.sh: /usr/local/bin/splitbytaxa.sh |
| 175 | + splitnextera.sh: /usr/local/bin/splitnextera.sh |
| 176 | + splitribo.sh: /usr/local/bin/splitribo.sh |
| 177 | + splitsam.sh: /usr/local/bin/splitsam.sh |
| 178 | + splitsam4way.sh: /usr/local/bin/splitsam4way.sh |
| 179 | + splitsam6way.sh: /usr/local/bin/splitsam6way.sh |
| 180 | + stats.sh: /usr/local/bin/stats.sh |
| 181 | + statswrapper.sh: /usr/local/bin/statswrapper.sh |
| 182 | + streamsam.sh: /usr/local/bin/streamsam.sh |
| 183 | + subsketch.sh: /usr/local/bin/subsketch.sh |
| 184 | + summarizecontam.sh: /usr/local/bin/summarizecontam.sh |
| 185 | + summarizecoverage.sh: /usr/local/bin/summarizecoverage.sh |
| 186 | + summarizecrossblock.sh: /usr/local/bin/summarizecrossblock.sh |
| 187 | + summarizemerge.sh: /usr/local/bin/summarizemerge.sh |
| 188 | + summarizequast.sh: /usr/local/bin/summarizequast.sh |
| 189 | + summarizescafstats.sh: /usr/local/bin/summarizescafstats.sh |
| 190 | + summarizeseal.sh: /usr/local/bin/summarizeseal.sh |
| 191 | + summarizesketch.sh: /usr/local/bin/summarizesketch.sh |
| 192 | + synthmda.sh: /usr/local/bin/synthmda.sh |
| 193 | + tadpipe.sh: /usr/local/bin/tadpipe.sh |
| 194 | + tadpole.sh: /usr/local/bin/tadpole.sh |
| 195 | + tadwrapper.sh: /usr/local/bin/tadwrapper.sh |
| 196 | + taxonomy.sh: /usr/local/bin/taxonomy.sh |
| 197 | + taxserver.sh: /usr/local/bin/taxserver.sh |
| 198 | + taxsize.sh: /usr/local/bin/taxsize.sh |
| 199 | + taxtree.sh: /usr/local/bin/taxtree.sh |
| 200 | + testfilesystem.sh: /usr/local/bin/testfilesystem.sh |
| 201 | + testformat.sh: /usr/local/bin/testformat.sh |
| 202 | + testformat2.sh: /usr/local/bin/testformat2.sh |
| 203 | + tetramerfreq.sh: /usr/local/bin/tetramerfreq.sh |
| 204 | + textfile.sh: /usr/local/bin/textfile.sh |
| 205 | + translate6frames.sh: /usr/local/bin/translate6frames.sh |
| 206 | + unicode2ascii.sh: /usr/local/bin/unicode2ascii.sh |
| 207 | + unzip.sh: /usr/local/bin/unzip.sh |
| 208 | + vcf2gff.sh: /usr/local/bin/vcf2gff.sh |
| 209 | + webcheck.sh: /usr/local/bin/webcheck.sh |
| 210 | + |
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