DownloadThis package includes BBMap, a short read aligner, as well as various other bioinformatic tools. It is written in pure Java, can run on any platform, and has no dependencies other than Java being installed (compiled for Java 6 and higher). All tools are efficient and multithreaded.
BBMap: Short read aligner for DNA and RNA-seq data. Capable of handling arbitrarily large genomes with millions of scaffolds. Handles Illumina, PacBio, 454, and other reads; very high sensitivity and tolerant of errors and numerous large indels. Very fast.
BBNorm: Kmer-based error-correction and normalization tool.
Dedupe: Simplifies assemblies by removing duplicate or contained subsequences that share a target percent identity.
Reformat: Reformats reads between fasta/fastq/scarf/fasta+qual/sam, interleaved/paired, and ASCII-33/64, at over 500 MB/s.
BBDuk: Filters, trims, or masks reads with kmer matches to an artifact/contaminant file.
...and more!
Features
- Pure Java, runs on any platform; already compiled, just unzip and run.
- Fast, efficient, and multithreaded.
- Usage information displayed when running a shellscript with no parameters.
- Highest sensitivity of any short-read aligner.
- Easy to install - just unzip/untar.
- Easy to use. Example: bbmap.sh ref=ecoli.fa in=reads.fq out=mapped.sam
- Handles all common formats: fasta, fastq, sam, scarf, fasta+qual, ASCII-33, ASCII-64, gzip.
- Used by the Joint Genome Institute.
- BB stands for Bestus Bioinformaticus.
- There is a handy FAQ here: http://seqanswers.com/forums/showthread.php?t=58221
Project Samples
User Reviews
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I was so tired of trimmomatic not doing what it was supposed to with the adapters, I found that I didn't have enough control with the exact settings for the adapter trimming. I downloaded Bbmap to use Bbduk and had it up and running in about 1 h of playing with the thresholds. Not only it did exactly what I needed ( I needed to cut an adaptors with the ability to specify if it was from the left or the right), but it was easy an intuitive to use.Reply from BBMapPosted 2022-08-30
Thanks for giving me my first review! I always like to hear that my tools do exactly what you need, and are intuitive and easy to use. Or, of course, if they aren't, so I can fix them. But I put a lot of effort into making them easy to use, so I'm glad it worked exactly as I intended. Well... sorry about the 1 hour of playing with thresholds, but yep, it can take that to optimize things for a custom case.