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bbtools mit Homebrew installieren

Prüfe Installationswege, Executables, Metadaten und Sicherheitshinweise für bbtools in AI-Agent-Workflows.

InstallationsbefehlSicherheitshinweise

Installation

Weitere Installationsbefehle

macOS

Homebrewverifiziert · 100%
brew install bbtools

local Homebrew formula metadata

Überblick

Paketzusammenfassung

Brian Bushnell's tools for manipulating reads

Befehle und Aliase

  • a_sample_mt.sh
  • addadapters.sh
  • addssu.sh
  • adjusthomopolymers.sh
  • alignrandom.sh
  • alltoall.sh
  • analyzeaccession.sh
  • analyzegenes.sh
  • analyzesketchresults.sh
  • applyvariants.sh
  • bamlinestreamer.sh
  • bandedaligner.sh
  • bandedplusaligner.sh
  • bbcms.sh
  • bbcountunique.sh
  • bbcrisprfinder.sh
  • bbduk.sh
  • bbdukOld.sh
  • bbdukS.sh
  • bbest.sh
  • bbfakereads.sh
  • bbmap.sh
  • bbmapskimmer.sh
  • bbmask.sh
  • bbmerge-auto.sh
  • bbmerge.sh
  • bbnorm.sh
  • bbrealign.sh
  • bbrename.sh
  • bbsketch.sh
  • bbsort.sh
  • bbsplit.sh

Verlauf

Projektgeschichte und Nutzung

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.

Projektgeschichte

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.

Adoptionsgeschichte

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.

Wie es verwendet wird

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.

Warum Paket-Nerds sich dafür interessieren

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.

Zeitleiste

  • 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.

Sicherheitslage

Noch keine Protected-Tool-Abdeckung gefunden

Für bbtools wurde kein passendes lokales Secret-Handling-Manifest gefunden. Nucleus-Paketmetadaten bleiben hier veröffentlicht, damit künftige Abdeckung eine stabile Paket-URL hat.

Installationsverhalten

  • In den Formelmetadaten ist kein Homebrew-Post-install-Hook erfasst.
  • Homebrew-Bottle-Metadaten sind für 6 Plattformziele verfügbar.
  • Installiert mit 1 Laufzeitabhängigkeiten.

Empfohlene Prüfung

Prüfe vor unbeaufsichtigter Agent-Nutzung, ob das Tool Klartext-Credentials liest, Remote-Zustand schreibt, Artefakte veröffentlicht oder Plugins ausführt.

local files

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

Config paths the tool may read or write during local use.

Unix
bbmap/config/

Executables

Installierte Executables

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

Aktualität

Version und Aktualität

Diese Signale trennen das Alter der Seitengenerierung, Aktivität des Paketmanagers und Upstream-Release-Vergleich. Versionsrückstand wird nur gemeldet, wenn eine Evidenz-URL und vergleichbare Versionen vorhanden sind.

Seite generiert2026-07-08
Manager-Version39.94
Manager aktualisiert2026-07-06
lokale DatenOK
Upstreamnot checked
neueste erkannte Versionnicht erkannt

https://bbmap.org/

  • InfoRelease/tag comparison is only available for GitHub repositories.https://bbmap.org/none Konfidenz

Installationsmetadaten

Paketmetadaten

Paketschlüsselbrew:bbtools
Version39.94
PaketmanagerHomebrew
Paketmanager-Seitehttps://formulae.brew.sh/formula/bbtools
Homepagehttps://bbmap.org/
Repositoryhttps://github.com/bbushnell/BBTools
Upstream-Dokumentationhttps://bbmap.org/docs
LizenzBSD-3-Clause
Quellarchivhttps://downloads.sourceforge.net/bbmap/BBMap_39.94.tar.gz
Zuletzt aktualisiert2026-07-06T08:10:17Z
Pulseupdated
Abhängigkeitenopenjdk
Bottleverfügbar (auf arm64_linux, arm64_sequoia, arm64_sonoma, arm64_tahoe, sonoma, x86_64_linux)
Homebrew post-installnicht definiert
Dienstkeiner deklariert

Registry-Fakten

Details aus der Quelldatenbank

Source DatabaseHomebrew formula API
Taphomebrew/core
Full Namebbtools
Version Scheme0
Revision0
Bottle Stable Root URLhttps://ghcr.io/v2/homebrew/core
Deprecatedno
Disabledno
Keg Onlyno
URL Keys
  • stable

Paketgraph

Links stammen aus dem lokalen Paketbeziehungsgraph, Ergänzungen, Abhängigkeitskanten, Ecosystem-Matches und Paket-Hub-Mitgliedschaft.

Verwandte Tools

  • openjdkRuntime dependency declared by Homebrew.

Gleicher Workflow

  • bowtie2Shares av.db curated category or tags: bioinformatics, cli, genomics, science, sequencing.
  • breseqShares av.db curated category or tags: bioinformatics, cli, dna, genomics, science.
  • fgbioShares av.db curated category or tags: bioinformatics, cli, genomics, science, sequencing.
  • htslibShares av.db curated category or tags: bioinformatics, cli, genomics, science, sequencing.
  • jellyfishShares av.db curated category or tags: bioinformatics, cli, dna, genomics, science.
  • kalignShares av.db curated category or tags: bioinformatics, cli, dna, rna, science.

Agent-Sicherheitsleitfäden

Quellspur

Aus Repository-Daten generiert

Diese Seite wird von av-web aus dem privaten Paket-SQLite-Artefakt bereitgestellt, das scripts/generate-pkg-sqlite.py erstellt.

Verwendete Quellen

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