# Installer bbtools avec Homebrew

Consultez les chemins d'installation, exécutables, métadonnées et notes de sécurité de bbtools pour les workflows d'agents IA.

## installation

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

Commandes d'installation supplémentaires:

### macOS

- Homebrew (100%):

```sh
brew install bbtools
```

  Preuve: local Homebrew formula metadata

## Faits du paquet

- **Clé du paquet:** brew:bbtools
- **Gestionnaire de paquets:** Homebrew
- **Version:** 40.01
- **Résumé source:** Brian Bushnell's tools for manipulating reads
- **Page d'accueil:** <https://bbmap.org/>
- **Dernière mise à jour:** 2026-08-03T09:05:47Z
- **Généré:** 2026-08-03T19:37:03+00:00

## exécutables

- a_sample_mt.sh (alias)
- addadapters.sh (alias)
- addssu.sh (alias)
- adjusthomopolymers.sh (alias)
- alignerbenchmark.sh (alias)
- alignrandom.sh (alias)
- alltoall.sh (alias)
- analyzeaccession.sh (alias)
- analyzegenes.sh (alias)
- analyzesketchresults.sh (alias)
- applyvariants.sh (alias)
- balancevectors.sh (alias)
- bamlinestreamer.sh (alias)
- bandedaligner.sh (alias)
- bandedplusaligner.sh (alias)
- bbcms.sh (alias)
- bbcountunique.sh (alias)
- bbcrisprfinder.sh (alias)
- bbduk.sh (alias)
- bbdukOld.sh (alias)
- bbdukS.sh (alias)
- bbest.sh (alias)
- bbfakereads.sh (alias)
- bbmap.sh (alias)
- bbmap5.sh (alias)
- bbmapacc.sh (alias)
- bbmapskimmer.sh (alias)
- bbmask.sh (alias)
- bbmerge-auto.sh (alias)
- bbmerge.sh (alias)
- bbnorm.sh (alias)
- bbrealign.sh (alias)
- bbrename.sh (alias)
- bbsketch.sh (alias)
- bbsort.sh (alias)
- bbsplit.sh (alias)
- bbsplitpairs.sh (alias)
- bbstats.sh (alias)
- bbversion.sh (alias)
- bbwrap.sh (alias)
- bedset.sh (alias)
- bloomfilter.sh (alias)
- bloomfilterparser.sh (alias)
- calcmem.sh (alias)
- calctruequality.sh (alias)
- callgenes.sh (alias)
- callpeaks.sh (alias)
- callvariants.sh (alias)
- callvariants2.sh (alias)
- cat.sh (alias)
- cbcl2text.sh (alias)
- cg2illumina.sh (alias)
- checkstrand.sh (alias)
- cladeloader.sh (alias)
- cladeserver.sh (alias)
- cloudplot.sh (alias)
- clumpify.sh (alias)
- commonkmers.sh (alias)
- comparegff.sh (alias)
- comparelabels.sh (alias)
- comparesketch.sh (alias)
- comparessu.sh (alias)
- comparevcf.sh (alias)
- consect.sh (alias)
- consensus.sh (alias)
- copyfile.sh (alias)
- countbarcodes.sh (alias)
- countbarcodes2.sh (alias)
- countduplicates.sh (alias)
- countgc.sh (alias)
- countsharedlines.sh (alias)
- covmaker.sh (alias)
- crossblock.sh (alias)
- crosscontaminate.sh (alias)
- crosscutaligner.sh (alias)
- cutgff.sh (alias)
- cutprimers.sh (alias)
- ddlblacklist.sh (alias)
- ddlcalibrate.sh (alias)
- ddlcompare.sh (alias)
- ddlmerger.sh (alias)
- ddlwriter.sh (alias)
- decontaminate.sh (alias)
- dedupe.sh (alias)
- dedupe2.sh (alias)
- dedupebymapping.sh (alias)
- demuxbyname.sh (alias)
- demuxserver.sh (alias)
- diskbench.sh (alias)
- dlctieraccuracy.sh (alias)
- driftingaligner.sh (alias)
- driftingplusaligner.sh (alias)
- estherfilter.sh (alias)
- explodetree.sh (alias)
- fastqscan.sh (alias)
- fetchproks.sh (alias)
- filescan.sh (alias)
- filterassemblysummary.sh (alias)
- filterbarcodes.sh (alias)
- filterbycoverage.sh (alias)
- filterbyname.sh (alias)
- filterbysequence.sh (alias)
- filterbytaxa.sh (alias)
- filterbytile.sh (alias)
- filterlines.sh (alias)
- filtersam.sh (alias)
- filtersilva.sh (alias)
- filtersubs.sh (alias)
- filtervcf.sh (alias)
- findrepeats.sh (alias)
- findssu.sh (alias)
- fix_script_paths.sh (alias)
- fixgaps.sh (alias)
- fll2simulate.sh (alias)
- fungalrelease.sh (alias)
- fuse.sh (alias)
- fusebytaxa.sh (alias)
- gbff2gff.sh (alias)
- getreads.sh (alias)
- gi2ancestors.sh (alias)
- gi2taxid.sh (alias)
- gitable.sh (alias)
- glocalaligner.sh (alias)
- gradebins.sh (alias)
- grademerge.sh (alias)
- gradesam.sh (alias)
- gradevcf.sh (alias)
- icecreamfinder.sh (alias)
- icecreamgrader.sh (alias)
- icecreammaker.sh (alias)
- idmatrix.sh (alias)
- idtree.sh (alias)
- indelfree.sh (alias)
- invertkey.sh (alias)
- invertvcf.sh (alias)
- javasetup.sh (alias)
- kapastats.sh (alias)
- kcompress.sh (alias)
- keepbestcopy.sh (alias)
- khist.sh (alias)
- kmercountexact.sh (alias)
- kmercountmulti.sh (alias)
- kmercountshort.sh (alias)
- kmercoverage.sh (alias)
- kmerfilterset.sh (alias)
- kmerhashdump.sh (alias)
- kmerlimit.sh (alias)
- kmerlimit2.sh (alias)
- kmerposition.sh (alias)
- kmutate.sh (alias)
- lilypad.sh (alias)
- loadreads.sh (alias)
- loglog.sh (alias)
- lowcomplexcalibrate.sh (alias)
- makechimeras.sh (alias)
- makecontaminatedgenomes.sh (alias)
- makepolymers.sh (alias)
- makequickbinvector.sh (alias)
- mantissacompare.sh (alias)
- mapPacBio.sh (alias)
- matrixtocolumns.sh (alias)
- memdetect.sh (alias)
- mergeOTUs.sh (alias)
- mergebarcodes.sh (alias)
- mergepgm.sh (alias)
- mergeribo.sh (alias)
- mergesam.sh (alias)
- mergesam2.sh (alias)
- mergesketch.sh (alias)
- mergesorted.sh (alias)
- microalign.sh (alias)
- msa.sh (alias)
- mutate.sh (alias)
- muxbyname.sh (alias)
- netconvert.sh (alias)
- netfilter.sh (alias)
- novademux.sh (alias)
- parallelogram.sh (alias)
- partition.sh (alias)
- phylip2fasta.sh (alias)
- picksubset.sh (alias)
- pileup.sh (alias)
- pileup2.sh (alias)
- plotflowcell.sh (alias)
- plotgc.sh (alias)
- plothist.sh (alias)
- plotreadposition.sh (alias)
- polyfilter.sh (alias)
- postfilter.sh (alias)
- printtime.sh (alias)
- processfrag.sh (alias)
- processhi-c.sh (alias)
- processspeed.sh (alias)
- profile.sh (alias)
- quabblealigner.sh (alias)
- quantumaligner.sh (alias)
- quickbin.sh (alias)
- quickclade.sh (alias)
- randomgenome.sh (alias)
- randomreads.sh (alias)
- randomreadsmg.sh (alias)
- readlength.sh (alias)
- reassemble.sh (alias)
- reducecolumns.sh (alias)
- reducesilva.sh (alias)
- reformat.sh (alias)
- reformat2.sh (alias)
- reformat3.sh (alias)
- reformatpb.sh (alias)
- removebadbarcodes.sh (alias)
- removecatdogmousehuman.sh (alias)
- removehuman.sh (alias)
- removehuman2.sh (alias)
- removemicrobes.sh (alias)
- removesmartbell.sh (alias)
- rename.sh (alias)
- renamebymapping.sh (alias)
- renamebysketch.sh (alias)
- renameimg.sh (alias)
- renameref.sh (alias)
- repair.sh (alias)
- replaceheaders.sh (alias)
- representative.sh (alias)
- restorebases.sh (alias)
- rqcfilter.sh (alias)
- rqcfilter2.sh (alias)
- rqcfilter3.sh (alias)
- runhmm.sh (alias)
- samstreamer.sh (alias)
- samtoroc.sh (alias)
- scalarintervals.sh (alias)
- scalars.sh (alias)
- scoresequence.sh (alias)
- scrabblealigner.sh (alias)
- seal.sh (alias)
- sendclade.sh (alias)
- sendsketch.sh (alias)
- seqtovec.sh (alias)
- shred.sh (alias)
- shrinkaccession.sh (alias)
- shuffle.sh (alias)
- shuffle2.sh (alias)
- sketch.sh (alias)
- sketchblacklist.sh (alias)
- sketchblacklist2.sh (alias)
- smithwaterman.sh (alias)
- sortbyname.sh (alias)
- splitbytaxa.sh (alias)
- splitnextera.sh (alias)
- splitribo.sh (alias)
- splitsam.sh (alias)
- splitsam4way.sh (alias)
- splitsam6way.sh (alias)
- ssuserver.sh (alias)
- stats.sh (alias)
- stats3.sh (alias)
- statswrapper.sh (alias)
- stream.sh (alias)
- streamsam.sh (alias)
- subsketch.sh (alias)
- summarizecontam.sh (alias)
- summarizecoverage.sh (alias)
- summarizecrossblock.sh (alias)
- summarizemerge.sh (alias)
- summarizequast.sh (alias)
- summarizescafstats.sh (alias)
- summarizeseal.sh (alias)
- summarizesketch.sh (alias)
- synthmda.sh (alias)
- tadpipe.sh (alias)
- tadpole.sh (alias)
- tadwrapper.sh (alias)
- tagandmerge.sh (alias)
- taxonomy.sh (alias)
- taxserver.sh (alias)
- taxsize.sh (alias)
- taxtree.sh (alias)
- testaligners.sh (alias)
- testaligners2.sh (alias)
- testalignersbatch.sh (alias)
- testalignerslength.sh (alias)
- testfilesystem.sh (alias)
- testformat.sh (alias)
- testformat2.sh (alias)
- tetramerfreq.sh (alias)
- textfile.sh (alias)
- tiledump.sh (alias)
- train.sh (alias)
- trainLCHist.sh (alias)
- translate6frames.sh (alias)
- trimcontigs.sh (alias)
- ttllsimulate.sh (alias)
- unicode2ascii.sh (alias)
- unzip.sh (alias)
- vcf2gff.sh (alias)
- vectorutils.sh (alias)
- visualizealignment.sh (alias)
- wavefrontaligner.sh (alias)
- wavefrontalignerviz.sh (alias)
- webcheck.sh (alias)
- wobblealigner.sh (alias)
- wobbleplusaligner.sh (alias)
- xdrophaligner.sh (alias)
- zz_rename_package.sh (alias)

## Comportement d'installation

- Bouteille: non disponible

## Version et fraîcheur

- page générée: 2026-08-03
- version du gestionnaire: 40.01
## Historique du projet et usages

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.

### Historique du projet

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.

### Historique d'adoption

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.

### Modes d'utilisation

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.

### Pourquoi les passionnés de paquets s'y intéressent

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.

### Chronologie

- 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.

### Sources

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


## Notes de sécurité

Aucun manifest local de gestion des secrets correspondant n'a été trouvé pour bbtools. Les métadonnées de paquet Nucleus restent publiées ici afin que la couverture future dispose d'une URL stable.



## 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/

## Combined YAML source

View the package source record on GitHub. [combined/bbtools.yml](https://github.com/mxcl/pkgdb/blob/main/combined/bbtools.yml)


## Sources

- pkg.so package database
- Geiger risk classifier
- curated configuration and credential file locations
- curated package history
- pkgdb category and tag curation
- cross-ecosystem install command graph