Dataset Information

Mosdepth: quick coverage calculation for genomes and exomes.

ABSTRACT:

Summary

Mosdepth is a new command-line tool for rapidly calculating genome-wide sequencing coverage. It measures depth from BAM or CRAM files at either each nucleotide position in a genome or for sets of genomic regions. Genomic regions may be specified as either a BED file to evaluate coverage across capture regions, or as a fixed-size window as required for copy-number calling. Mosdepth uses a simple algorithm that is computationally efficient and enables it to quickly produce coverage summaries. We demonstrate that mosdepth is faster than existing tools and provides flexibility in the types of coverage profiles produced.

Availability and implementation

mosdepth is available from https://github.com/brentp/mosdepth under the MIT license.

Contact

bpederse@gmail.com.

Supplementary information

Supplementary data are available at Bioinformatics online.

SUBMITTER: Pedersen BS

PROVIDER: S-EPMC6030888 | biostudies-literature | 2018 Mar

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Mosdepth: quick coverage calculation for genomes and exomes.

Pedersen Brent S BS Quinlan Aaron R AR

Bioinformatics (Oxford, England) 20180301 5

<h4>Summary</h4>Mosdepth is a new command-line tool for rapidly calculating genome-wide sequencing coverage. It measures depth from BAM or CRAM files at either each nucleotide position in a genome or for sets of genomic regions. Genomic regions may be specified as either a BED file to evaluate coverage across capture regions, or as a fixed-size window as required for copy-number calling. Mosdepth uses a simple algorithm that is computationally efficient and enables it to quickly produce coverage ...[more]

PMID: 29096012

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Dataset Information

Mosdepth: quick coverage calculation for genomes and exomes.

Summary

Availability and implementation

Contact

Supplementary information

Publications

Mosdepth: quick coverage calculation for genomes and exomes.

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