mosdepth

Mosdepth is a command-line tool used to measure depth from BAM or CRAM files in order to rapidly calculate genome-wide sequencing coverage. It can measure depth at each nucleotide position in a genome or for sets of genomic regions specified in a BED file. Mosdepth is computationally efficient and faster than existing tools, providing flexibility in the types of coverage profiles produced.

Topic

Statistics and probability;Data quality management

Detail

  • Operation: Nucleic acid sequence analysis;Read depth analysis

  • Software interface: Command-line user interface

  • Language: Shell

  • License: The MIT licence

  • Cost: Free

  • Version name: v0.3.3

  • Credit: The US National Human Genome Research Institute (NIH), the US National Institute of General Medical Sciences, the US National Cancer Institute (NIH).

  • Input: BAM, CRAM

  • Output: -

  • Contact: bpederse@gmail.com

  • Collection: -

  • Maturity: -

Publications

  • Mosdepth: quick coverage calculation for genomes and exomes.
  • Pedersen BS and Quinlan AR. Mosdepth: quick coverage calculation for genomes and exomes. Mosdepth: quick coverage calculation for genomes and exomes. 2018; 34:867-868. doi: 10.1093/bioinformatics/btx699
  • https://doi.org/10.1093/bioinformatics/btx699
  • PMID: 29096012
  • PMC: PMC6030888

Download and documentation

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