|
Name |
|
Date |
Size |
#Lines |
LOC |
| .. | | 03-May-2022 | - |
| config/ | H | 03-May-2022 | - | | |
| current/ | H | 11-Aug-2021 | - | 375,565 | 267,566 |
| docs/guides/ | H | 03-May-2022 | - | | |
| jni/ | H | 03-May-2022 | - | 2,978 | 2,325 |
| pipelines/ | H | 04-May-2020 | - | 1,515 | 611 |
| pytools/ | H | 04-Apr-2020 | - | 9,646 | 6,321 |
| resources/ | H | 03-May-2022 | - | 449,689 | 449,646 |
| README.md | H A D | 19-Jul-2021 | 216 | 7 | 5 |
| a_sample_mt.sh | H A D | 03-May-2022 | 2.1 KiB | 84 | 65 |
| addadapters.sh | H A D | 03-May-2022 | 2.6 KiB | 79 | 61 |
| addssu.sh | H A D | 03-May-2022 | 2.2 KiB | 95 | 72 |
| adjusthomopolymers.sh | H A D | 03-May-2022 | 2.1 KiB | 82 | 63 |
| alltoall.sh | H A D | 03-May-2022 | 2 KiB | 80 | 62 |
| analyzeaccession.sh | H A D | 03-May-2022 | 1.5 KiB | 64 | 47 |
| analyzegenes.sh | H A D | 03-May-2022 | 1.4 KiB | 63 | 46 |
| analyzesketchresults.sh | H A D | 03-May-2022 | 2.2 KiB | 76 | 56 |
| applyvariants.sh | H A D | 03-May-2022 | 2.6 KiB | 92 | 73 |
| bbcms.sh | H A D | 03-May-2022 | 6.3 KiB | 151 | 126 |
| bbcountunique.sh | H A D | 03-May-2022 | 2.8 KiB | 94 | 74 |
| bbduk.sh | H A D | 03-May-2022 | 19.3 KiB | 369 | 338 |
| bbest.sh | H A D | 03-May-2022 | 1.4 KiB | 62 | 45 |
| bbfakereads.sh | H A D | 03-May-2022 | 2.9 KiB | 83 | 63 |
| bbmap.sh | H A D | 03-May-2022 | 19.6 KiB | 358 | 327 |
| bbmapskimmer.sh | H A D | 03-May-2022 | 1.1 KiB | 55 | 40 |
| bbmask.sh | H A D | 03-May-2022 | 4.4 KiB | 111 | 89 |
| bbmerge-auto.sh | H A D | 03-May-2022 | 1.3 KiB | 60 | 47 |
| bbmerge.sh | H A D | 03-May-2022 | 13.6 KiB | 262 | 231 |
| bbnorm.sh | H A D | 03-May-2022 | 9.8 KiB | 168 | 143 |
| bbrealign.sh | H A D | 03-May-2022 | 3.3 KiB | 109 | 88 |
| bbrename.sh | H A D | 03-May-2022 | 406 | 19 | 10 |
| bbsketch.sh | H A D | 03-May-2022 | 466 | 20 | 10 |
| bbsplit.sh | H A D | 03-May-2022 | 5.9 KiB | 132 | 107 |
| bbsplitpairs.sh | H A D | 03-May-2022 | 3.3 KiB | 83 | 63 |
| bbstats.sh | H A D | 03-May-2022 | 402 | 19 | 10 |
| bbversion.sh | H A D | 03-May-2022 | 527 | 33 | 24 |
| bbwrap.sh | H A D | 03-May-2022 | 2 KiB | 78 | 60 |
| bitbucket-pipelines.yml | H A D | 12-Jun-2020 | 594 | 18 | 16 |
| bloomfilter.sh | H A D | 03-May-2022 | 3.7 KiB | 109 | 88 |
| build.xml | H A D | 09-Oct-2020 | 2 KiB | 57 | 38 |
| calcmem.sh | H A D | 03-May-2022 | 4.7 KiB | 190 | 120 |
| calctruequality.sh | H A D | 03-May-2022 | 5.6 KiB | 153 | 123 |
| callgenes.sh | H A D | 03-May-2022 | 2.3 KiB | 85 | 63 |
| callpeaks.sh | H A D | 03-May-2022 | 2.3 KiB | 77 | 59 |
| callvariants.sh | H A D | 03-May-2022 | 9.2 KiB | 209 | 183 |
| callvariants2.sh | H A D | 03-May-2022 | 1.4 KiB | 57 | 38 |
| clumpify.sh | H A D | 03-May-2022 | 11.4 KiB | 235 | 209 |
| commonkmers.sh | H A D | 03-May-2022 | 1.8 KiB | 71 | 53 |
| comparegff.sh | H A D | 03-May-2022 | 1.1 KiB | 63 | 47 |
| comparesketch.sh | H A D | 03-May-2022 | 14.6 KiB | 295 | 263 |
| comparessu.sh | H A D | 03-May-2022 | 2.5 KiB | 90 | 70 |
| comparevcf.sh | H A D | 03-May-2022 | 2.3 KiB | 87 | 68 |
| consect.sh | H A D | 03-May-2022 | 1.9 KiB | 75 | 57 |
| consensus.sh | H A D | 03-May-2022 | 3.3 KiB | 102 | 80 |
| countbarcodes.sh | H A D | 03-May-2022 | 2.3 KiB | 78 | 59 |
| countgc.sh | H A D | 03-May-2022 | 1.2 KiB | 59 | 43 |
| countsharedlines.sh | H A D | 03-May-2022 | 2.1 KiB | 77 | 60 |
| crossblock.sh | H A D | 03-May-2022 | 157 | 12 | 5 |
| crosscontaminate.sh | H A D | 03-May-2022 | 2.9 KiB | 94 | 75 |
| cutgff.sh | H A D | 03-May-2022 | 3 KiB | 91 | 71 |
| cutprimers.sh | H A D | 03-May-2022 | 2 KiB | 80 | 61 |
| decontaminate.sh | H A D | 03-May-2022 | 4.9 KiB | 129 | 104 |
| dedupe.sh | H A D | 03-May-2022 | 9 KiB | 171 | 144 |
| dedupe2.sh | H A D | 03-May-2022 | 1.3 KiB | 64 | 50 |
| dedupebymapping.sh | H A D | 03-May-2022 | 2.5 KiB | 84 | 66 |
| demuxbyname.sh | H A D | 03-May-2022 | 7.4 KiB | 153 | 127 |
| diskbench.sh | H A D | 03-May-2022 | 1.8 KiB | 74 | 56 |
| estherfilter.sh | H A D | 03-May-2022 | 1.3 KiB | 61 | 43 |
| explodetree.sh | H A D | 03-May-2022 | 1.6 KiB | 67 | 50 |
| fetchproks.sh | H A D | 03-May-2022 | 1.9 KiB | 71 | 53 |
| filterassemblysummary.sh | H A D | 03-May-2022 | 3.1 KiB | 96 | 77 |
| filterbarcodes.sh | H A D | 03-May-2022 | 2.7 KiB | 82 | 63 |
| filterbycoverage.sh | H A D | 03-May-2022 | 2.6 KiB | 83 | 66 |
| filterbyname.sh | H A D | 03-May-2022 | 3.7 KiB | 106 | 85 |
| filterbysequence.sh | H A D | 03-May-2022 | 2.4 KiB | 84 | 66 |
| filterbytaxa.sh | H A D | 03-May-2022 | 3.9 KiB | 112 | 92 |
| filterbytile.sh | H A D | 03-May-2022 | 4.4 KiB | 123 | 101 |
| filterlines.sh | H A D | 03-May-2022 | 2.5 KiB | 83 | 65 |
| filterqc.sh | H A D | 03-May-2022 | 1.9 KiB | 86 | 66 |
| filtersam.sh | H A D | 03-May-2022 | 2.6 KiB | 88 | 70 |
| filtersilva.sh | H A D | 03-May-2022 | 1.5 KiB | 74 | 52 |
| filtersubs.sh | H A D | 03-May-2022 | 1.5 KiB | 63 | 46 |
| filtervcf.sh | H A D | 03-May-2022 | 3.6 KiB | 112 | 91 |
| fixgaps.sh | H A D | 03-May-2022 | 2.3 KiB | 84 | 66 |
| fungalrelease.sh | H A D | 03-May-2022 | 2.7 KiB | 92 | 74 |
| fuse.sh | H A D | 03-May-2022 | 2.4 KiB | 84 | 67 |
| gbff2gff.sh | H A D | 03-May-2022 | 856 | 51 | 37 |
| getreads.sh | H A D | 03-May-2022 | 1.2 KiB | 59 | 43 |
| gi2ancestors.sh | H A D | 03-May-2022 | 1.8 KiB | 76 | 58 |
| gi2taxid.sh | H A D | 03-May-2022 | 3 KiB | 98 | 79 |
| gitable.sh | H A D | 03-May-2022 | 1.9 KiB | 73 | 56 |
| grademerge.sh | H A D | 03-May-2022 | 981 | 47 | 32 |
| gradesam.sh | H A D | 03-May-2022 | 1.6 KiB | 53 | 38 |
| icecreamfinder.sh | H A D | 03-May-2022 | 6 KiB | 149 | 127 |
| icecreamgrader.sh | H A D | 03-May-2022 | 1 KiB | 57 | 41 |
| icecreammaker.sh | H A D | 03-May-2022 | 3.6 KiB | 112 | 90 |
| idmatrix.sh | H A D | 03-May-2022 | 2.3 KiB | 85 | 67 |
| idtree.sh | H A D | 03-May-2022 | 1.7 KiB | 77 | 59 |
| invertkey.sh | H A D | 03-May-2022 | 1.6 KiB | 75 | 56 |
| kapastats.sh | H A D | 03-May-2022 | 1.6 KiB | 68 | 51 |
| kcompress.sh | H A D | 03-May-2022 | 3.4 KiB | 104 | 83 |
| keepbestcopy.sh | H A D | 03-May-2022 | 2 KiB | 82 | 63 |
| khist.sh | H A D | 03-May-2022 | 1.1 KiB | 57 | 43 |
| kmercountexact.sh | H A D | 03-May-2022 | 5.9 KiB | 147 | 120 |
| kmercountmulti.sh | H A D | 03-May-2022 | 2.6 KiB | 85 | 67 |
| kmercoverage.sh | H A D | 03-May-2022 | 4.1 KiB | 103 | 83 |
| kmerfilterset.sh | H A D | 03-May-2022 | 2.6 KiB | 86 | 67 |
| kmerlimit.sh | H A D | 03-May-2022 | 2.6 KiB | 86 | 67 |
| kmerlimit2.sh | H A D | 03-May-2022 | 2.6 KiB | 87 | 68 |
| kmerposition.sh | H A D | 03-May-2022 | 1.8 KiB | 73 | 54 |
| kmutate.sh | H A D | 03-May-2022 | 4 KiB | 120 | 95 |
| lilypad.sh | H A D | 03-May-2022 | 2.6 KiB | 90 | 72 |
| loadreads.sh | H A D | 03-May-2022 | 1.5 KiB | 72 | 55 |
| loglog.sh | H A D | 03-May-2022 | 2.3 KiB | 84 | 64 |
| makechimeras.sh | H A D | 03-May-2022 | 1.8 KiB | 77 | 59 |
| makecontaminatedgenomes.sh | H A D | 03-May-2022 | 2.2 KiB | 82 | 64 |
| makepolymers.sh | H A D | 03-May-2022 | 2.1 KiB | 81 | 63 |
| mapPacBio.sh | H A D | 03-May-2022 | 1.7 KiB | 77 | 63 |
| matrixtocolumns.sh | H A D | 03-May-2022 | 1.5 KiB | 68 | 52 |
| mergeOTUs.sh | H A D | 03-May-2022 | 1 KiB | 53 | 38 |
| mergebarcodes.sh | H A D | 03-May-2022 | 2.6 KiB | 88 | 67 |
| mergepgm.sh | H A D | 03-May-2022 | 1.3 KiB | 62 | 46 |
| mergeribo.sh | H A D | 03-May-2022 | 3.3 KiB | 101 | 83 |
| mergesam.sh | H A D | 03-May-2022 | 1,003 | 55 | 39 |
| mergesketch.sh | H A D | 03-May-2022 | 2.9 KiB | 100 | 79 |
| mergesorted.sh | H A D | 03-May-2022 | 2.8 KiB | 96 | 76 |
| msa.sh | H A D | 03-May-2022 | 2.5 KiB | 89 | 72 |
| mutate.sh | H A D | 03-May-2022 | 3.3 KiB | 101 | 83 |
| muxbyname.sh | H A D | 03-May-2022 | 2.1 KiB | 79 | 60 |
| partition.sh | H A D | 03-May-2022 | 2.1 KiB | 76 | 56 |
| phylip2fasta.sh | H A D | 03-May-2022 | 1.7 KiB | 76 | 57 |
| pileup.sh | H A D | 03-May-2022 | 7.3 KiB | 156 | 133 |
| plotflowcell.sh | H A D | 03-May-2022 | 2.7 KiB | 94 | 74 |
| plotgc.sh | H A D | 03-May-2022 | 1.9 KiB | 79 | 61 |
| postfilter.sh | H A D | 03-May-2022 | 2.8 KiB | 95 | 75 |
| printtime.sh | H A D | 03-May-2022 | 943 | 50 | 36 |
| processfrag.sh | H A D | 03-May-2022 | 1.4 KiB | 65 | 48 |
| processhi-c.sh | H A D | 03-May-2022 | 2 KiB | 72 | 55 |
| processspeed.sh | H A D | 03-May-2022 | 936 | 52 | 36 |
| randomgenome.sh | H A D | 03-May-2022 | 1.5 KiB | 65 | 49 |
| randomreads.sh | H A D | 03-May-2022 | 7.3 KiB | 177 | 151 |
| readlength.sh | H A D | 03-May-2022 | 1.5 KiB | 61 | 45 |
| readqc.sh | H A D | 03-May-2022 | 1.5 KiB | 73 | 52 |
| reducesilva.sh | H A D | 03-May-2022 | 1.9 KiB | 73 | 55 |
| reformat.sh | H A D | 03-May-2022 | 13.8 KiB | 234 | 199 |
| reformatpb.sh | H A D | 03-May-2022 | 5 KiB | 137 | 113 |
| removebadbarcodes.sh | H A D | 03-May-2022 | 1.8 KiB | 72 | 54 |
| removecatdogmousehuman.sh | H A D | 03-May-2022 | 2.5 KiB | 77 | 59 |
| removehuman.sh | H A D | 03-May-2022 | 2.5 KiB | 75 | 57 |
| removehuman2.sh | H A D | 03-May-2022 | 2.5 KiB | 71 | 54 |
| removemicrobes.sh | H A D | 03-May-2022 | 2.9 KiB | 82 | 63 |
| removesmartbell.sh | H A D | 03-May-2022 | 1.3 KiB | 61 | 44 |
| rename.sh | H A D | 03-May-2022 | 3.5 KiB | 95 | 75 |
| renameimg.sh | H A D | 03-May-2022 | 1.7 KiB | 66 | 49 |
| repair.sh | H A D | 03-May-2022 | 2.9 KiB | 91 | 73 |
| replaceheaders.sh | H A D | 03-May-2022 | 2.5 KiB | 80 | 61 |
| representative.sh | H A D | 03-May-2022 | 3.3 KiB | 101 | 83 |
| rqcfilter.sh | H A D | 03-May-2022 | 403 | 19 | 10 |
| rqcfilter2.sh | H A D | 03-May-2022 | 13.4 KiB | 268 | 226 |
| runhmm.sh | H A D | 03-May-2022 | 1 KiB | 62 | 42 |
| samtoroc.sh | H A D | 03-May-2022 | 1.9 KiB | 68 | 50 |
| seal.sh | H A D | 03-May-2022 | 11 KiB | 224 | 200 |
| sendsketch.sh | H A D | 03-May-2022 | 12.2 KiB | 273 | 240 |
| shred.sh | H A D | 03-May-2022 | 1.6 KiB | 61 | 45 |
| shrinkaccession.sh | H A D | 03-May-2022 | 1.7 KiB | 69 | 51 |
| shuffle.sh | H A D | 03-May-2022 | 2.3 KiB | 83 | 64 |
| shuffle2.sh | H A D | 03-May-2022 | 2.3 KiB | 81 | 63 |
| sketch.sh | H A D | 03-May-2022 | 6.5 KiB | 157 | 134 |
| sketchblacklist.sh | H A D | 03-May-2022 | 3.5 KiB | 103 | 85 |
| sketchblacklist2.sh | H A D | 03-May-2022 | 3.2 KiB | 100 | 82 |
| sortbyname.sh | H A D | 03-May-2022 | 2.8 KiB | 100 | 79 |
| splitbytaxa.sh | H A D | 03-May-2022 | 2.7 KiB | 93 | 73 |
| splitnextera.sh | H A D | 03-May-2022 | 3.7 KiB | 103 | 78 |
| splitribo.sh | H A D | 03-May-2022 | 2.4 KiB | 88 | 69 |
| splitsam.sh | H A D | 03-May-2022 | 1.1 KiB | 53 | 39 |
| splitsam4way.sh | H A D | 03-May-2022 | 988 | 50 | 36 |
| splitsam6way.sh | H A D | 03-May-2022 | 1,000 | 50 | 36 |
| stats.sh | H A D | 03-May-2022 | 3.8 KiB | 110 | 88 |
| statswrapper.sh | H A D | 03-May-2022 | 2.3 KiB | 75 | 58 |
| streamsam.sh | H A D | 03-May-2022 | 1.7 KiB | 69 | 53 |
| subsketch.sh | H A D | 03-May-2022 | 2.2 KiB | 82 | 63 |
| summarizecontam.sh | H A D | 03-May-2022 | 2 KiB | 81 | 63 |
| summarizecoverage.sh | H A D | 03-May-2022 | 1.4 KiB | 61 | 44 |
| summarizecrossblock.sh | H A D | 03-May-2022 | 1.8 KiB | 71 | 53 |
| summarizemerge.sh | H A D | 03-May-2022 | 1 KiB | 56 | 39 |
| summarizequast.sh | H A D | 03-May-2022 | 1.2 KiB | 59 | 42 |
| summarizescafstats.sh | H A D | 03-May-2022 | 1.6 KiB | 65 | 47 |
| summarizeseal.sh | H A D | 03-May-2022 | 2.1 KiB | 75 | 56 |
| summarizesketch.sh | H A D | 03-May-2022 | 1.4 KiB | 61 | 43 |
| synthmda.sh | H A D | 03-May-2022 | 2.4 KiB | 87 | 69 |
| tadpipe.sh | H A D | 03-May-2022 | 1.8 KiB | 84 | 64 |
| tadpole.sh | H A D | 03-May-2022 | 12.1 KiB | 249 | 217 |
| tadwrapper.sh | H A D | 03-May-2022 | 1.6 KiB | 73 | 57 |
| taxonomy.sh | H A D | 03-May-2022 | 3.1 KiB | 100 | 80 |
| taxserver.sh | H A D | 03-May-2022 | 3.9 KiB | 118 | 89 |
| taxsize.sh | H A D | 03-May-2022 | 1.5 KiB | 66 | 49 |
| taxtree.sh | H A D | 03-May-2022 | 1.6 KiB | 72 | 55 |
| testfilesystem.sh | H A D | 03-May-2022 | 1 KiB | 56 | 39 |
| testformat.sh | H A D | 03-May-2022 | 1.1 KiB | 57 | 40 |
| testformat2.sh | H A D | 03-May-2022 | 4.7 KiB | 151 | 115 |
| tetramerfreq.sh | H A D | 03-May-2022 | 2 KiB | 80 | 62 |
| textfile.sh | H A D | 03-May-2022 | 1,000 | 52 | 38 |
| translate6frames.sh | H A D | 03-May-2022 | 2.7 KiB | 95 | 74 |
| unicode2ascii.sh | H A D | 03-May-2022 | 1.1 KiB | 54 | 39 |
| unzip.sh | H A D | 03-May-2022 | 1.3 KiB | 62 | 45 |
| vcf2gff.sh | H A D | 03-May-2022 | 901 | 54 | 38 |
| webcheck.sh | H A D | 03-May-2022 | 1.8 KiB | 72 | 54 |
README.md
1# BBTools bioinformatics tools, including BBMap.
2# Author: Brian Bushnell, Jon Rood, Shijie Yao, Jasper Toscani Field
3# Language: Java, Bash
4# Information about documentation is in /docs/readme.txt.
5
6# Version 38.91
7