BBMap short read aligner, and other bioinformatic tools

What is BBMap? To quote the webpage:

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. …and more!

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will add those to the path.

  1. The BBMap project is entirely written in Java. This does not necessarily play well with batch system. Please have a look on our hints to Java or approach us and report specific issues1).
  2. Mapping software can cause I/O contention. We can check your jobscript, if in doubt.

There are no wrapper scripts in place. So, when launching them concurrently please be sure to avoid I/O contention (e.g. stage-in data to a local disk or ramdisk). You can approach us, if you want to integrate any of those tools into your workflow.

Issues with regard to the application itself should be reported to the developer
  • software/topical/lifescience/bbmap.txt
  • Last modified: 2018/09/09 16:58
  • by meesters