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bbmap website  

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.

Environment Modules

Run module spider bbmap to find out what environment modules are available for this application.

System Variables

  • HPC_BBMAP_DIR - installation directory
  • HPC_BBMAP_BIN - executable directory
  • HPC_BBMAP_DOC - documentation directory (docs/)
  • HPC_BBMAP_RES - resource directory (resources/)
  • HPC_BBMAP_CONF - configuration directory (config/)