Year: 2017
Type: article
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: [email protected]. Supplementary information: Supplementary data are available at Bioinformatics online.
Source: Bioinformatics
Authors: Brent S Pedersen, Aaron R Quinlan
Institution: University of Utah
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: hybrid
Estimated APC paid: $3,989
OpenAlex ID: W2950006249