The OFFICIAL Suite of Bioinformatics Tools
Fast, multithreaded tools for DNA and RNA sequence analysis
Interactive web interfaces for BBTools analysis - no installation required!
Rapid taxonomic classification using kmer frequency comparison. Identify organisms from DNA sequences in seconds.
Fast sequence identification using MinHash sketches. Compare sequences against RefSeq, Silva, and other databases.
Interactive visualization of sequence alignments. Compare 9 different alignment algorithms with beautiful graphics.
Fast short read aligner optimized for variant calling from Illumina data. Handles reads up to 6kbp.
bbmap.sh ref=genome.fa in=reads.fq out=mapped.sam
Adapter trimming, quality filtering, and contaminant removal. The Swiss Army knife of read processing.
bbduk.sh in=reads.fq out=clean.fq ref=adapters.fa ktrim=r k=23 mink=11 hdist=1 tpe tbo
Paired read merging using neural networks for very low false positive rates.
bbmerge.sh in1=r1.fq in2=r2.fq out=merged.fq outu=unmerged.fq
Fast error correction and assembly for small genomes, amplicons, and metagenomes.
tadpole.sh in=reads.fq out=corrected.fq mode=correct
Reorders reads to reduce file size by 30% on average. Also finds and removes duplicates without alignment.
clumpify.sh in=reads.fq out=clumped.fq.gz
Kmer-based normalization to reduce coverage variation for better assemblies.
bbnorm.sh in=reads.fq out=normalized.fq target=100
Error correction and low-depth removal for metagenomes with no memory constraints.
bbcms.sh in=reads.fq out=corrected.fq
Rapid taxonomic identification by comparing MinHash sketches to remote databases.
sendsketch.sh in=unknown.fa
High-speed alignment-free sequence quantification for RNA-seq using kmer matching.
seal.sh in=reads.fq ref=transcripts.fa rpkm=rpkm.txt
Bins metagenomic contigs using coverage and kmer frequencies for metagenome analysis.
quickbin.sh in=contigs.fa out=bins *.sam
Fast taxonomic assignment using kmer frequency spectra, optimized for metagenomic bins.
quickclade.sh bins out=taxonomy.tsv
Statistical demultiplexing with error correction for optimal yield and minimal crosstalk.
novademux.sh in=reads.fq out=out_%.fq expected=barcodes.txt
Variant calling from SAM/BAM files with multisample VCF support.
callvariants.sh in=mapped.sam ref=genome.fa vcf=vars.vcf
Gene prediction for prokaryotes, viruses, and mitochondria. Also finds 16S/18S/23S/5S/tRNAs.
callgenes.sh in=contigs.fa out=genes.gff outa=aminos.faa
Sort reads by name, length, quality, position, taxonomy, or other keys. Handles any file size.
sortbyname.sh in=reads.fq out=sorted.fq
Multithreaded, memory-efficient algorithms with SIMD support
Over 90 tools covering alignment, assembly, QC, and analysis
BBMap created by Brian Bushnell; suite expanded at JGI. Cited in thousands of publications
Handles FASTQ, FASTA, SAM/BAM, and compressed files seamlessly
Current Version: 39.34
License: Free for unlimited use
PLOS ONE 12(10): e0185056 (2017)
Neural network-based approach for merging paired-end sequencing reads with very low false positive rates.
DOI: 10.1371/journal.pone.0185056Preprint (2025)
Ultra-fast metagenomic read simulation tool for generating realistic synthetic datasets at terabase scale.
Preprint AvailableMore publications coming soon! BBTools are actively used in research worldwide.
If you use BBTools in your research, please cite:
Bushnell, B. (2014) BBMap: A Fast, Accurate, Splice-Aware Aligner. 9th Annual Genomics of Energy & Environment Meeting, Walnut Creek, CA. BBTools software package: https://bbmap.org GitHub: https://github.com/bbushnell/BBTools ORCID: https://orcid.org/0000-0002-8140-0131
For BBMerge specifically:
Bushnell B, Rood J, Singer E (2017) BBMerge – Accurate paired shotgun read merging via overlap. PLoS ONE 12(10): e0185056. DOI: 10.1371/journal.pone.0185056