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bazam

  • Description

    is a tool to extract paired reads in FASTQ format from coordinate sorted BAM files.

    Bazam is a smarter way to realign reads from one genome to another. If you've tried to use Picard SAMtoFASTQ or samtools bam2fq before and ended up unsatisfied with complicated, long running inefficient pipelines, bazam might be what you wanted. Bazam will output FASTQ in a form that can stream directly into common aligners such as BWA or Bowtie2, so that you can quickly and easily realign reads without extraction to any intermediate format. Bazam can target a specific region of the genome, specified as a region or a gene name if you prefer.

  • Usage

    To list all executables provided by bazam, run: $ biogrids-list bazam Copy to clipboard

  • Installation

    Use the following command to install this title with the CLI client: $ biogrids-cli install bazam Copy to clipboard Available operating systems: Linux 64, OS X INTEL

  • Primary Citation*

    S. P. Sadedin and O. A.. 2019. Bazam: a rapid method for read extraction and realignment of high-throughput sequencing data. Genome Biol.. 20(1): 78.


    • *Full citation information available through

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