BWA MEM for single or paired end reads and own genome


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
  • 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.