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brew

Install bbtools with Homebrew

Brian Bushnell's tools for manipulating reads. Version 39.94 via Homebrew; verified 2026-07-06.

Install commandSecurity notes

install

Additional install commands

macOS

Homebrewverified ยท 100%
brew install bbtools

local Homebrew formula metadata

overview

Package summary

Brian Bushnell's tools for manipulating reads

Commands and aliases

  • 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

history

Project history and usage

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.

Project history

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.

Adoption history

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.

How it is used

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.

Why package nerds care

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.

Timeline

  • 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.

security posture

No protected-tool coverage found yet

No matching local secret-handling manifest was found for bbtools. Nucleus package metadata is still published here so future coverage has a stable package URL.

Install behavior

  • No Homebrew post-install hook is recorded in formula metadata.
  • Homebrew bottle metadata is available for 6 platform targets.
  • Installs with 1 runtime dependencies.

Recommended review

Before unattended agent use, check whether the tool reads plaintext credentials, writes remote state, publishes artifacts, or shells out to plugins.

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

Installed executables

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

freshness

Version and freshness

These signals separate page generation age, package-manager activity, and upstream release comparison. Version lag is warned only when an evidence URL and comparable versions are present.

page generated2026-07-08
manager version39.94
manager updated2026-07-06
local dataok
upstreamnot checked
latest detectednot detected

https://bbmap.org/

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

install metadata

Package metadata

Package keybrew:bbtools
Version39.94
Package managerHomebrew
Package manager pagehttps://formulae.brew.sh/formula/bbtools
Homepagehttps://bbmap.org/
Repositoryhttps://github.com/bbushnell/BBTools
Upstream docshttps://bbmap.org/docs
LicenseBSD-3-Clause
Source archivehttps://downloads.sourceforge.net/bbmap/BBMap_39.94.tar.gz
Last updated2026-07-06T08:10:17Z
Pulseupdated
Dependenciesopenjdk
Bottleavailable (on arm64_linux, arm64_sequoia, arm64_sonoma, arm64_tahoe, sonoma, x86_64_linux)
Homebrew post-installnot defined
Servicenone declared

registry facts

Source database details

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

package graph

Links come from deterministic package relationships, av.db category and tag curation, ecosystem matches, and package hub membership.

Related tools

  • openjdkRuntime dependency declared by Homebrew.

Same 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.

source trail

Generated from repository data

This page is generated by av-web from the private package SQLite artifact built by scripts/generate-pkg-sqlite.py.

Used sources

  • 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