BWA MEM for single or paired end reads


This tool aligns single end reads or paired-end reads to selected reference genome using the BWA MEM algorithm. The reads have to be supplied in fastq format. If just one reads file is defined then single-end analysis is performed. If two reads files are defined, then paired end analysis is performed.

Alignment parameters

Read group parameters

  • More information: BWA manual
  • Output

    As a result the tool returns a sorted and indexed BAM-formatted alignment, which is ready for viewing in the Chipster genome browser.