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bwa-pssm website  

BWA-PSSM is a probabilistic short read aligner based on the use of position specific scoring matrices (PSSM). Like many of the existing aligners it is fast and sensitive. Unlike most other aligners, however, it also adaptible in the sense that one can direct the alignment based on known biases within the data set. It is coded as a modification of the original BWA alignment program and shares the genome index structure as well as many of the command line options.

Environment Modules

Run module spider bwa-pssm to find out what environment modules are available for this application.

System Variables

  • HPC_BWA-PSSM_DIR - installation directory
  • HPC_BWA-PSSM_BIN - executable directory


If you publish research that uses bwa-pssm you have to cite it as follows:

Kerpedjiev, P., Frellsen, J., Lindgreen, S., & Krogh, A. (2014). Adaptable probabilistic mapping of short reads using position specific scoring matrices. BMC bioinformatics, 15(1), 100.