BWA MEM for single or paired end reads and own genome

Description

This tool aligns single end reads or paired-end reads to the reference genome sequence given by the user. The reads have to be supplied in fastq format. If two input files is selected, one of the file is used as a reference genome and the another one is used as the reads file for single-end alignment. If three input 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.