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.

Alignment parameters

Read group parameters

  • More information: BWA manual
  • Details

    It is possible to give the tool more than one FASTQ file/file pair. The tool will run the alignment for each file/file pair separately, and finally merge the resulting BAM files.

    If you provide two FASTQ files, the tool will by default perform a paired-end alignment with them. It will try assign R1 and R2 reads correctly by file name.

    If you have more than two FASTQ files (or wish to perform single-end alignment for two files), you will need to provide a list of filenames of the FASTQ files; one list for single-end alignment, and two for paired-end alignment (one file for R1 files, and another one for the R2 files) as a text file (e.g.R1files.txt and R2files.txt). These lists can be generated with the tool Utilities / Make a list of file names . The read pairs must be ordered identically in both lists.

    To run, select the list file/files (R1files.txt and R2files.txt) and ALL FASTQ files, and assign the list files correctly. When assigning the list files, they are automatically inactivated in the "Reads" file list.


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