This is the Windows app named BBMap whose latest release can be downloaded as BBMap_38.95.tar.gz. It can be run online in the free hosting provider OnWorks for workstations.
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This 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.
- 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
This is an application that can also be fetched from https://sourceforge.net/projects/bbmap/. It has been hosted in OnWorks in order to be run online in an easiest way from one of our free Operative Systems.