# bbtools を Homebrew でインストール

bbtools のインストール経路、実行ファイル、メタデータ、AI エージェント向けセキュリティノートを確認します。

## インストール

```sh
sudo av install brew:bbtools
```

追加のインストールコマンド:

### macOS

- Homebrew (100%):

```sh
brew install bbtools
```

  証拠: local Homebrew formula metadata

## パッケージ情報

- **パッケージキー:** brew:bbtools
- **パッケージマネージャ:** Homebrew
- **パッケージマネージャページ:** <https://formulae.brew.sh/formula/bbtools>
- **バージョン:** 39.94
- **ソース概要:** Brian Bushnell's tools for manipulating reads
- **ホームページ:** <https://bbmap.org/>
- **リポジトリ:** <https://github.com/bbushnell/BBTools>
- **上流ドキュメント:** <https://bbmap.org/docs>
- **ライセンス:** BSD-3-Clause
- **ソースアーカイブ:** <https://downloads.sourceforge.net/bbmap/BBMap_39.94.tar.gz>
- **最終更新:** 2026-07-06T08:10:17Z
- **生成日時:** 2026-07-08T07:18:31+00:00

## 実行可能ファイル

- a_sample_mt.sh (cli)
- addadapters.sh (cli)
- addssu.sh (cli)
- adjusthomopolymers.sh (cli)
- alignrandom.sh (cli)
- alltoall.sh (cli)
- analyzeaccession.sh (cli)
- analyzegenes.sh (cli)
- analyzesketchresults.sh (cli)
- applyvariants.sh (cli)
- bamlinestreamer.sh (cli)
- bandedaligner.sh (cli)
- bandedplusaligner.sh (cli)
- bbcms.sh (cli)
- bbcountunique.sh (cli)
- bbcrisprfinder.sh (cli)
- bbduk.sh (cli)
- bbdukOld.sh (cli)
- bbdukS.sh (cli)
- bbest.sh (cli)
- bbfakereads.sh (cli)
- bbmap.sh (cli)
- bbmapskimmer.sh (cli)
- bbmask.sh (cli)
- bbmerge-auto.sh (cli)
- bbmerge.sh (cli)
- bbnorm.sh (cli)
- bbrealign.sh (cli)
- bbrename.sh (cli)
- bbsketch.sh (cli)
- bbsort.sh (cli)
- bbsplit.sh (cli)
- bbsplitpairs.sh (cli)
- bbstats.sh (cli)
- bbversion.sh (cli)
- bbwrap.sh (cli)
- bloomfilter.sh (cli)
- bloomfilterparser.sh (cli)
- calcmem.sh (cli)
- calctruequality.sh (cli)
- callgenes.sh (cli)
- callpeaks.sh (cli)
- callvariants.sh (cli)
- callvariants2.sh (cli)
- cat.sh (cli)
- cbcl2text.sh (cli)
- cg2illumina.sh (cli)
- checkstrand.sh (cli)
- cladeloader.sh (cli)
- cladeserver.sh (cli)
- cloudplot.sh (cli)
- clumpify.sh (cli)
- commonkmers.sh (cli)
- comparegff.sh (cli)
- comparelabels.sh (cli)
- comparesketch.sh (cli)
- comparessu.sh (cli)
- comparevcf.sh (cli)
- consect.sh (cli)
- consensus.sh (cli)
- copyfile.sh (cli)
- countbarcodes.sh (cli)
- countbarcodes2.sh (cli)
- countduplicates.sh (cli)
- countgc.sh (cli)
- countsharedlines.sh (cli)
- covmaker.sh (cli)
- crossblock.sh (cli)
- crosscontaminate.sh (cli)
- crosscutaligner.sh (cli)
- cutgff.sh (cli)
- cutprimers.sh (cli)
- ddlblacklist.sh (cli)
- ddlcalibrate.sh (cli)
- ddlcompare.sh (cli)
- ddlmerger.sh (cli)
- ddlwriter.sh (cli)
- decontaminate.sh (cli)
- dedupe.sh (cli)
- dedupe2.sh (cli)
- dedupebymapping.sh (cli)
- demuxbyname.sh (cli)
- demuxserver.sh (cli)
- diskbench.sh (cli)
- dlctieraccuracy.sh (cli)
- driftingaligner.sh (cli)
- driftingplusaligner.sh (cli)
- estherfilter.sh (cli)
- explodetree.sh (cli)
- fastqscan.sh (cli)
- fetchproks.sh (cli)
- filescan.sh (cli)
- filterassemblysummary.sh (cli)
- filterbarcodes.sh (cli)
- filterbycoverage.sh (cli)
- filterbyname.sh (cli)
- filterbysequence.sh (cli)
- filterbytaxa.sh (cli)
- filterbytile.sh (cli)
- filterlines.sh (cli)
- filtersam.sh (cli)
- filtersilva.sh (cli)
- filtersubs.sh (cli)
- filtervcf.sh (cli)
- findrepeats.sh (cli)
- findssu.sh (cli)
- fix_script_paths.sh (cli)
- fixgaps.sh (cli)
- fll2simulate.sh (cli)
- fungalrelease.sh (cli)
- fuse.sh (cli)
- gbff2gff.sh (cli)
- getreads.sh (cli)
- gi2ancestors.sh (cli)
- gi2taxid.sh (cli)
- gitable.sh (cli)
- glocalaligner.sh (cli)
- gradebins.sh (cli)
- grademerge.sh (cli)
- gradesam.sh (cli)
- icecreamfinder.sh (cli)
- icecreamgrader.sh (cli)
- icecreammaker.sh (cli)
- idmatrix.sh (cli)
- idtree.sh (cli)
- indelfree.sh (cli)
- invertkey.sh (cli)
- javasetup.sh (cli)
- kapastats.sh (cli)
- kcompress.sh (cli)
- keepbestcopy.sh (cli)
- khist.sh (cli)
- kmercountexact.sh (cli)
- kmercountmulti.sh (cli)
- kmercountshort.sh (cli)
- kmercoverage.sh (cli)
- kmerfilterset.sh (cli)
- kmerlimit.sh (cli)
- kmerlimit2.sh (cli)
- kmerposition.sh (cli)
- kmutate.sh (cli)
- lilypad.sh (cli)
- loadreads.sh (cli)
- loglog.sh (cli)
- lowcomplexcalibrate.sh (cli)
- makechimeras.sh (cli)
- makecontaminatedgenomes.sh (cli)
- makepolymers.sh (cli)
- makequickbinvector.sh (cli)
- mantissacompare.sh (cli)
- mapPacBio.sh (cli)
- matrixtocolumns.sh (cli)
- memdetect.sh (cli)
- mergeOTUs.sh (cli)
- mergebarcodes.sh (cli)
- mergepgm.sh (cli)
- mergeribo.sh (cli)
- mergesam.sh (cli)
- mergesketch.sh (cli)
- mergesorted.sh (cli)
- microalign.sh (cli)
- msa.sh (cli)
- mutate.sh (cli)
- muxbyname.sh (cli)
- netfilter.sh (cli)
- novademux.sh (cli)
- parallelogram.sh (cli)
- partition.sh (cli)
- phylip2fasta.sh (cli)
- picksubset.sh (cli)
- pileup.sh (cli)
- pileup2.sh (cli)
- plotflowcell.sh (cli)
- plotgc.sh (cli)
- plothist.sh (cli)
- plotreadposition.sh (cli)
- polyfilter.sh (cli)
- postfilter.sh (cli)
- printtime.sh (cli)
- processfrag.sh (cli)
- processhi-c.sh (cli)
- processspeed.sh (cli)
- profile.sh (cli)
- quabblealigner.sh (cli)
- quantumaligner.sh (cli)
- quickbin.sh (cli)
- quickclade.sh (cli)
- randomgenome.sh (cli)
- randomreads.sh (cli)
- randomreadsmg.sh (cli)
- readlength.sh (cli)
- reassemble.sh (cli)
- reducecolumns.sh (cli)
- reducesilva.sh (cli)
- reformat.sh (cli)
- reformat2.sh (cli)
- reformat3.sh (cli)
- reformatpb.sh (cli)
- removebadbarcodes.sh (cli)
- removecatdogmousehuman.sh (cli)
- removehuman.sh (cli)
- removehuman2.sh (cli)
- removemicrobes.sh (cli)
- removesmartbell.sh (cli)
- rename.sh (cli)
- renamebymapping.sh (cli)
- renamebysketch.sh (cli)
- renameimg.sh (cli)
- renameref.sh (cli)
- repair.sh (cli)
- replaceheaders.sh (cli)
- representative.sh (cli)
- rqcfilter.sh (cli)
- rqcfilter2.sh (cli)
- rqcfilter3.sh (cli)
- runhmm.sh (cli)
- samstreamer.sh (cli)
- samtoroc.sh (cli)
- scalarintervals.sh (cli)
- scalars.sh (cli)
- scoresequence.sh (cli)
- scrabblealigner.sh (cli)
- seal.sh (cli)
- sendclade.sh (cli)
- sendsketch.sh (cli)
- seqtovec.sh (cli)
- shred.sh (cli)
- shrinkaccession.sh (cli)
- shuffle.sh (cli)
- shuffle2.sh (cli)
- sketch.sh (cli)
- sketchblacklist.sh (cli)
- sketchblacklist2.sh (cli)
- smithwaterman.sh (cli)
- sortbyname.sh (cli)
- splitbytaxa.sh (cli)
- splitnextera.sh (cli)
- splitribo.sh (cli)
- splitsam.sh (cli)
- splitsam4way.sh (cli)
- splitsam6way.sh (cli)
- ssuserver.sh (cli)
- stats.sh (cli)
- stats3.sh (cli)
- statswrapper.sh (cli)
- stream.sh (cli)
- streamsam.sh (cli)
- subsketch.sh (cli)
- summarizecontam.sh (cli)
- summarizecoverage.sh (cli)
- summarizecrossblock.sh (cli)
- summarizemerge.sh (cli)
- summarizequast.sh (cli)
- summarizescafstats.sh (cli)
- summarizeseal.sh (cli)
- summarizesketch.sh (cli)
- synthmda.sh (cli)
- tadpipe.sh (cli)
- tadpole.sh (cli)
- tadwrapper.sh (cli)
- tagandmerge.sh (cli)
- taxonomy.sh (cli)
- taxserver.sh (cli)
- taxsize.sh (cli)
- taxtree.sh (cli)
- testaligners.sh (cli)
- testaligners2.sh (cli)
- testalignersbatch.sh (cli)
- testalignerslength.sh (cli)
- testfilesystem.sh (cli)
- testformat.sh (cli)
- testformat2.sh (cli)
- tetramerfreq.sh (cli)
- textfile.sh (cli)
- tiledump.sh (cli)
- train.sh (cli)
- trainLCHist.sh (cli)
- translate6frames.sh (cli)
- trimcontigs.sh (cli)
- ttllsimulate.sh (cli)
- unicode2ascii.sh (cli)
- unzip.sh (cli)
- vcf2gff.sh (cli)
- visualizealignment.sh (cli)
- wavefrontaligner.sh (cli)
- wavefrontalignerviz.sh (cli)
- webcheck.sh (cli)
- wobblealigner.sh (cli)
- wobbleplusaligner.sh (cli)
- xdrophaligner.sh (cli)
- zz_rename_package.sh (cli)
- a_sample_mt.sh (エイリアス)
- addadapters.sh (エイリアス)
- addssu.sh (エイリアス)
- adjusthomopolymers.sh (エイリアス)
- alignrandom.sh (エイリアス)
- alltoall.sh (エイリアス)
- analyzeaccession.sh (エイリアス)
- analyzegenes.sh (エイリアス)
- analyzesketchresults.sh (エイリアス)
- applyvariants.sh (エイリアス)
- bamlinestreamer.sh (エイリアス)
- bandedaligner.sh (エイリアス)
- bandedplusaligner.sh (エイリアス)
- bbcms.sh (エイリアス)
- bbcountunique.sh (エイリアス)
- bbcrisprfinder.sh (エイリアス)
- bbduk.sh (エイリアス)
- bbdukOld.sh (エイリアス)
- bbdukS.sh (エイリアス)
- bbest.sh (エイリアス)
- bbfakereads.sh (エイリアス)
- bbmap.sh (エイリアス)
- bbmapskimmer.sh (エイリアス)
- bbmask.sh (エイリアス)
- bbmerge-auto.sh (エイリアス)
- bbmerge.sh (エイリアス)
- bbnorm.sh (エイリアス)
- bbrealign.sh (エイリアス)
- bbrename.sh (エイリアス)
- bbsketch.sh (エイリアス)
- bbsort.sh (エイリアス)
- bbsplit.sh (エイリアス)
- bbsplitpairs.sh (エイリアス)
- bbstats.sh (エイリアス)
- bbversion.sh (エイリアス)
- bbwrap.sh (エイリアス)
- bloomfilter.sh (エイリアス)
- bloomfilterparser.sh (エイリアス)
- calcmem.sh (エイリアス)
- calctruequality.sh (エイリアス)
- callgenes.sh (エイリアス)
- callpeaks.sh (エイリアス)
- callvariants.sh (エイリアス)
- callvariants2.sh (エイリアス)
- cat.sh (エイリアス)
- cbcl2text.sh (エイリアス)
- cg2illumina.sh (エイリアス)
- checkstrand.sh (エイリアス)
- cladeloader.sh (エイリアス)
- cladeserver.sh (エイリアス)
- cloudplot.sh (エイリアス)
- clumpify.sh (エイリアス)
- commonkmers.sh (エイリアス)
- comparegff.sh (エイリアス)
- comparelabels.sh (エイリアス)
- comparesketch.sh (エイリアス)
- comparessu.sh (エイリアス)
- comparevcf.sh (エイリアス)
- consect.sh (エイリアス)
- consensus.sh (エイリアス)
- copyfile.sh (エイリアス)
- countbarcodes.sh (エイリアス)
- countbarcodes2.sh (エイリアス)
- countduplicates.sh (エイリアス)
- countgc.sh (エイリアス)
- countsharedlines.sh (エイリアス)
- covmaker.sh (エイリアス)
- crossblock.sh (エイリアス)
- crosscontaminate.sh (エイリアス)
- crosscutaligner.sh (エイリアス)
- cutgff.sh (エイリアス)
- cutprimers.sh (エイリアス)
- ddlblacklist.sh (エイリアス)
- ddlcalibrate.sh (エイリアス)
- ddlcompare.sh (エイリアス)
- ddlmerger.sh (エイリアス)
- ddlwriter.sh (エイリアス)
- decontaminate.sh (エイリアス)
- dedupe.sh (エイリアス)
- dedupe2.sh (エイリアス)
- dedupebymapping.sh (エイリアス)
- demuxbyname.sh (エイリアス)
- demuxserver.sh (エイリアス)
- diskbench.sh (エイリアス)
- dlctieraccuracy.sh (エイリアス)
- driftingaligner.sh (エイリアス)
- driftingplusaligner.sh (エイリアス)
- estherfilter.sh (エイリアス)
- explodetree.sh (エイリアス)
- fastqscan.sh (エイリアス)
- fetchproks.sh (エイリアス)
- filescan.sh (エイリアス)
- filterassemblysummary.sh (エイリアス)
- filterbarcodes.sh (エイリアス)
- filterbycoverage.sh (エイリアス)
- filterbyname.sh (エイリアス)
- filterbysequence.sh (エイリアス)
- filterbytaxa.sh (エイリアス)
- filterbytile.sh (エイリアス)
- filterlines.sh (エイリアス)
- filtersam.sh (エイリアス)
- filtersilva.sh (エイリアス)
- filtersubs.sh (エイリアス)
- filtervcf.sh (エイリアス)
- findrepeats.sh (エイリアス)
- findssu.sh (エイリアス)
- fix_script_paths.sh (エイリアス)
- fixgaps.sh (エイリアス)
- fll2simulate.sh (エイリアス)
- fungalrelease.sh (エイリアス)
- fuse.sh (エイリアス)
- gbff2gff.sh (エイリアス)
- getreads.sh (エイリアス)
- gi2ancestors.sh (エイリアス)
- gi2taxid.sh (エイリアス)
- gitable.sh (エイリアス)
- glocalaligner.sh (エイリアス)
- gradebins.sh (エイリアス)
- grademerge.sh (エイリアス)
- gradesam.sh (エイリアス)
- icecreamfinder.sh (エイリアス)
- icecreamgrader.sh (エイリアス)
- icecreammaker.sh (エイリアス)
- idmatrix.sh (エイリアス)
- idtree.sh (エイリアス)
- indelfree.sh (エイリアス)
- invertkey.sh (エイリアス)
- javasetup.sh (エイリアス)
- kapastats.sh (エイリアス)
- kcompress.sh (エイリアス)
- keepbestcopy.sh (エイリアス)
- khist.sh (エイリアス)
- kmercountexact.sh (エイリアス)
- kmercountmulti.sh (エイリアス)
- kmercountshort.sh (エイリアス)
- kmercoverage.sh (エイリアス)
- kmerfilterset.sh (エイリアス)
- kmerlimit.sh (エイリアス)
- kmerlimit2.sh (エイリアス)
- kmerposition.sh (エイリアス)
- kmutate.sh (エイリアス)
- lilypad.sh (エイリアス)
- loadreads.sh (エイリアス)
- loglog.sh (エイリアス)
- lowcomplexcalibrate.sh (エイリアス)
- makechimeras.sh (エイリアス)
- makecontaminatedgenomes.sh (エイリアス)
- makepolymers.sh (エイリアス)
- makequickbinvector.sh (エイリアス)
- mantissacompare.sh (エイリアス)
- mapPacBio.sh (エイリアス)
- matrixtocolumns.sh (エイリアス)
- memdetect.sh (エイリアス)
- mergeOTUs.sh (エイリアス)
- mergebarcodes.sh (エイリアス)
- mergepgm.sh (エイリアス)
- mergeribo.sh (エイリアス)
- mergesam.sh (エイリアス)
- mergesketch.sh (エイリアス)
- mergesorted.sh (エイリアス)
- microalign.sh (エイリアス)
- msa.sh (エイリアス)
- mutate.sh (エイリアス)
- muxbyname.sh (エイリアス)
- netfilter.sh (エイリアス)
- novademux.sh (エイリアス)
- parallelogram.sh (エイリアス)
- partition.sh (エイリアス)
- phylip2fasta.sh (エイリアス)
- picksubset.sh (エイリアス)
- pileup.sh (エイリアス)
- pileup2.sh (エイリアス)
- plotflowcell.sh (エイリアス)
- plotgc.sh (エイリアス)
- plothist.sh (エイリアス)
- plotreadposition.sh (エイリアス)
- polyfilter.sh (エイリアス)
- postfilter.sh (エイリアス)
- printtime.sh (エイリアス)
- processfrag.sh (エイリアス)
- processhi-c.sh (エイリアス)
- processspeed.sh (エイリアス)
- profile.sh (エイリアス)
- quabblealigner.sh (エイリアス)
- quantumaligner.sh (エイリアス)
- quickbin.sh (エイリアス)
- quickclade.sh (エイリアス)
- randomgenome.sh (エイリアス)
- randomreads.sh (エイリアス)
- randomreadsmg.sh (エイリアス)
- readlength.sh (エイリアス)
- reassemble.sh (エイリアス)
- reducecolumns.sh (エイリアス)
- reducesilva.sh (エイリアス)
- reformat.sh (エイリアス)
- reformat2.sh (エイリアス)
- reformat3.sh (エイリアス)
- reformatpb.sh (エイリアス)
- removebadbarcodes.sh (エイリアス)
- removecatdogmousehuman.sh (エイリアス)
- removehuman.sh (エイリアス)
- removehuman2.sh (エイリアス)
- removemicrobes.sh (エイリアス)
- removesmartbell.sh (エイリアス)
- rename.sh (エイリアス)
- renamebymapping.sh (エイリアス)
- renamebysketch.sh (エイリアス)
- renameimg.sh (エイリアス)
- renameref.sh (エイリアス)
- repair.sh (エイリアス)
- replaceheaders.sh (エイリアス)
- representative.sh (エイリアス)
- rqcfilter.sh (エイリアス)
- rqcfilter2.sh (エイリアス)
- rqcfilter3.sh (エイリアス)
- runhmm.sh (エイリアス)
- samstreamer.sh (エイリアス)
- samtoroc.sh (エイリアス)
- scalarintervals.sh (エイリアス)
- scalars.sh (エイリアス)
- scoresequence.sh (エイリアス)
- scrabblealigner.sh (エイリアス)
- seal.sh (エイリアス)
- sendclade.sh (エイリアス)
- sendsketch.sh (エイリアス)
- seqtovec.sh (エイリアス)
- shred.sh (エイリアス)
- shrinkaccession.sh (エイリアス)
- shuffle.sh (エイリアス)
- shuffle2.sh (エイリアス)
- sketch.sh (エイリアス)
- sketchblacklist.sh (エイリアス)
- sketchblacklist2.sh (エイリアス)
- smithwaterman.sh (エイリアス)
- sortbyname.sh (エイリアス)
- splitbytaxa.sh (エイリアス)
- splitnextera.sh (エイリアス)
- splitribo.sh (エイリアス)
- splitsam.sh (エイリアス)
- splitsam4way.sh (エイリアス)
- splitsam6way.sh (エイリアス)
- ssuserver.sh (エイリアス)
- stats.sh (エイリアス)
- stats3.sh (エイリアス)
- statswrapper.sh (エイリアス)
- stream.sh (エイリアス)
- streamsam.sh (エイリアス)
- subsketch.sh (エイリアス)
- summarizecontam.sh (エイリアス)
- summarizecoverage.sh (エイリアス)
- summarizecrossblock.sh (エイリアス)
- summarizemerge.sh (エイリアス)
- summarizequast.sh (エイリアス)
- summarizescafstats.sh (エイリアス)
- summarizeseal.sh (エイリアス)
- summarizesketch.sh (エイリアス)
- synthmda.sh (エイリアス)
- tadpipe.sh (エイリアス)
- tadpole.sh (エイリアス)
- tadwrapper.sh (エイリアス)
- tagandmerge.sh (エイリアス)
- taxonomy.sh (エイリアス)
- taxserver.sh (エイリアス)
- taxsize.sh (エイリアス)
- taxtree.sh (エイリアス)
- testaligners.sh (エイリアス)
- testaligners2.sh (エイリアス)
- testalignersbatch.sh (エイリアス)
- testalignerslength.sh (エイリアス)
- testfilesystem.sh (エイリアス)
- testformat.sh (エイリアス)
- testformat2.sh (エイリアス)
- tetramerfreq.sh (エイリアス)
- textfile.sh (エイリアス)
- tiledump.sh (エイリアス)
- train.sh (エイリアス)
- trainLCHist.sh (エイリアス)
- translate6frames.sh (エイリアス)
- trimcontigs.sh (エイリアス)
- ttllsimulate.sh (エイリアス)
- unicode2ascii.sh (エイリアス)
- unzip.sh (エイリアス)
- vcf2gff.sh (エイリアス)
- visualizealignment.sh (エイリアス)
- wavefrontaligner.sh (エイリアス)
- wavefrontalignerviz.sh (エイリアス)
- webcheck.sh (エイリアス)
- wobblealigner.sh (エイリアス)
- wobbleplusaligner.sh (エイリアス)
- xdrophaligner.sh (エイリアス)
- zz_rename_package.sh (エイリアス)

## 依存関係

- openjdk

## インストール挙動

- post-install フック: 未定義
- Bottle: 利用可能 対象 arm64_linux, arm64_sequoia, arm64_sonoma, arm64_tahoe, sonoma, x86_64_linux

## バージョンと鮮度

- ページ生成日: 2026-07-08
- マネージャ版: 39.94
- マネージャ更新日: 2026-07-06
- ローカルデータ: OK
- 上流リポジトリ: https://bbmap.org/
- 情報: Release/tag comparison is only available for GitHub repositories.
## プロジェクトの歴史と使われ方

BBTools is Brian Bushnell's large Java-based suite for DNA and RNA sequencing data. The suite includes BBMap, BBDuk, BBMerge, BBNorm, Tadpole, Clumpify, CallVariants, sketching tools, and many other command-line utilities.

### プロジェクトの歴史

The official site identifies BBMap and BBTools as the official suite created and maintained by Brian Bushnell. The GitHub README describes BBTools as fast, multithreaded bioinformatics tools for common sequencing formats including FASTQ, FASTA, SAM/BAM, GFF/GTF, VCF, and compressed files.

The package grew from core read-mapping and read-processing utilities into a broad toolbox. The official site lists hundreds of tools, while the README highlights core workflows such as adapter trimming, read mapping, error correction, assembly, compression optimization, variant calling, and MinHash-style sketch comparison.

The upstream README lists the current version as 39.93 and states that BBTools is used in production at JGI and cited in thousands of publications.

### 採用の歴史

BBTools' adoption is anchored in genomics labs and sequencing pipelines rather than general developer workflows. Its official download paths include GitHub, SourceForge, and Docker, while Homebrew packages it for macOS and Linux users who want the command suite installed alongside other scientific CLI tools.

### 使われ方

Common usage is pipeline-oriented: run scripts such as `bbduk.sh` for adapter trimming and quality filtering, `bbmap.sh` for short-read alignment, `bbmerge.sh` for paired-read merging, `tadpole.sh` for correction or small assembly, and `sendsketch.sh` for rapid organism identification.

Because it is Java-based and shell-script driven, BBTools is portable across Unix-like systems and easy to embed in HPC, workflow-manager, and lab automation environments.

### パッケージ好きにとっての重要性

BBTools matters to package nerds because it is a dense scientific tool suite distributed as many small executables from one upstream project. It is a good example of why package managers sometimes need to expose an entire research toolkit rather than one binary.

It also illustrates the packaging tension around bioinformatics software: users need reproducible versions, hundreds of entry points, Java runtime assumptions, documentation, and citation metadata, all for tools that may be critical to published scientific pipelines.

### タイムライン

- 2014: README citation names `BBMap: A Fast, Accurate, Splice-Aware Aligner`.
- Current: Official README lists BBTools version 39.93.
- Current: Official website describes BBMap/BBTools as Brian Bushnell's maintained suite and links GitHub, SourceForge, and Docker distribution paths.

### Related projects

- Related projects include BWA, Bowtie2, SAMtools, FastQC, Trimmomatic, Cutadapt, SPAdes, Kraken-style taxonomic tools, and other sequencing QC, alignment, assembly, and classification packages.

### ソース

- <https://bbmap.org/>
- <https://bbmap.org/tools>
- <https://github.com/bbushnell/BBTools#readme>
- input:source_facts.executables


## セキュリティノート

bbtools に一致するローカルシークレット処理マニフェストは見つかりませんでした。将来の対応で安定したパッケージ URL を使えるよう、Nucleus パッケージメタデータはここに公開されています。



## Configuration and credential file locations

These source-backed paths show where this package keeps local settings or durable credentials. Automic Vault can use them as review targets for secret scanning, migration, and command approval.


## Configuration files

- Unix: bbmap/config/
## ソースデータベース詳細

- **Source Database:** Homebrew formula API
- **Tap:** homebrew/core
- **Full Name:** bbtools
- **Version Scheme:** 0
- **Revision:** 0
- **Bottle Stable Root URL:** <https://ghcr.io/v2/homebrew/core>
- **Deprecated:** no
- **Disabled:** no
- **Keg Only:** no
- **URL Keys:** stable


## 関連リンク

- [Terminal utility packages](https://www.automicvault.com/ja/pkg/terminal-utilities/) - Matched terminal and command-line workflow metadata.
- [Networking and protocol packages](https://www.automicvault.com/ja/pkg/networking-protocol-tools/) - Matched network, protocol, or remote-service metadata.
- [Scientific computing packages](https://www.automicvault.com/ja/pkg/scientific-computing-tools/) - Matched scientific computing metadata.
- [Homebrew utility packages](https://www.automicvault.com/ja/pkg/brew-utility-packages/) - Matched Homebrew package provider.
- [openjdk](https://www.automicvault.com/ja/pkg/brew/openjdk/) - Runtime dependency declared by Homebrew.
- [bowtie2](https://www.automicvault.com/ja/pkg/brew/bowtie2/) - Shares av.db curated category or tags: bioinformatics, cli, genomics, science, sequencing.
- [breseq](https://www.automicvault.com/ja/pkg/brew/breseq/) - Shares av.db curated category or tags: bioinformatics, cli, dna, genomics, science.
- [fgbio](https://www.automicvault.com/ja/pkg/brew/fgbio/) - Shares av.db curated category or tags: bioinformatics, cli, genomics, science, sequencing.
- [htslib](https://www.automicvault.com/ja/pkg/brew/htslib/) - Shares av.db curated category or tags: bioinformatics, cli, genomics, science, sequencing.
- [jellyfish](https://www.automicvault.com/ja/pkg/brew/jellyfish/) - Shares av.db curated category or tags: bioinformatics, cli, dna, genomics, science.
- [kalign](https://www.automicvault.com/ja/pkg/brew/kalign/) - Shares av.db curated category or tags: bioinformatics, cli, dna, rna, science.
- [lastz](https://www.automicvault.com/ja/pkg/brew/lastz/) - Shares av.db curated category or tags: bioinformatics, cli, dna, genomics, science.
- [minimap2](https://www.automicvault.com/ja/pkg/brew/minimap2/) - Shares av.db curated category or tags: bioinformatics, cli, dna, genomics, science.
- [picard-tools](https://www.automicvault.com/ja/pkg/brew/picard-tools/) - Local package facts share a topical domain. Shared terms: bioinformatics, cli, genomics, manipulating, openjdk.
- [samtools](https://www.automicvault.com/ja/pkg/brew/samtools/) - Local package facts share a topical domain. Shared terms: bioinformatics, cli, genomics, manipulating, science.

## Combined YAML source

View the package source record on GitHub. [combined/bbtools.yml](https://github.com/automic-vault/db/blob/main/combined/bbtools.yml)


## ソース

- Nucleus package database
- Geiger risk classifier
- package-page enrichment
- curated configuration and credential file locations
- curated package history
- package version freshness
- av.db category and tag curation
- package relationship graph
- cross-ecosystem install command graph