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bwa-mem2 website  

We are happy to announce that the index size on disk is down by 8 times and in memory by 4 times due to moving to only one type of FM-index (2bit.64 instead of 2bit.64 and 8bit.32) and 8x compression of suffix array. For example, for human genome, index size on disk is down to ~10GB from ~80GB and memory footprint is down to ~10GB from ~40GB. There is a substantial reduction in index IO time due to the reduction and hardly any performance impact on read mapping. Due to this change in index structure (in commit #4b59796, 10th October 2020), you will need to rebuild the index.

Environment Modules

Run module spider bwa-mem2 to find out what environment modules are available for this application.

System Variables

  • HPC_BWA-MEM2_DIR - installation directory
  • HPC_BWA-MEM2_BIN - executable directory


If you publish research that uses bwa-mem2 you have to cite it as follows:

Vasimuddin Md, Sanchit Misra, Heng Li, Srinivas Aluru. Efficient Architecture-Aware Acceleration of BWA-MEM for Multicore Systems. IEEE Parallel and Distributed Processing Symposium (IPDPS), 2019.