Mosdepth: quick coverage calculation for genomes and exomes

By Brent S. Pedersen, Aaron R. Quinlan. bioRxiv, 2017

1,045 citations recorded by the source corpus.

Mosdepth is a new command-line tool for rapidly calculating genome-wide sequencing coverage. It measures depth from BAM (Li et al. 2009) 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 optional coverage summaries. We demonstrate that mosdepth is faster than existing tools and provides flexibility in the types of coverage profiles produced. Availability mosdepth is available from https://github.com/brentp/mosdepth under the MIT license‥ Contact bpederse@gmail.com, aaronquinlan@gmail.com Supplementary information Detailed documentation is available at https://github.com/brentp/mosdepth

Subfields: Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/bef6c45f5726647d971102295c0b9b2753ff52a4

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Genetics

In Molecular Biology

Citations in the corpus

CoverM: read alignment statistics for metagenomics (2025, neutral): “Notably, “Mosdepth arrays” were shown to be two times faster than naive methods for exact calculation of mean coverage (Pedersen and Quinlan 2018).”
Petabase-scale sequence alignment catalyses viral discovery (2020, methodology): “Finally mosdepth [71] was used to calculate a coverage pileup for each palmprint hit region within micro-assembled contigs.”