TY  - JOUR
TI  - Megadepth: efficient coverage quantification for BigWigs and BAMs
A1  - Wilks, C
A1  - Ahmed, O
A1  - Baker, DN
A1  - Zhang, D
A1  - Collado-Torres, L
A1  - Langmead, B
Y1  - 2021/09/15/
UR  - https://doi.org/10.1093/bioinformatics/btab152
N2  - Motivation
A common way to summarize sequencing datasets is to quantify data lying within genes or other genomic intervals. This can be slow and can require different tools for different input file types.

Results
Megadepth is a fast tool for quantifying alignments and coverage for BigWig and BAM/CRAM input files, using substantially less memory than the next-fastest competitor. Megadepth can summarize coverage within all disjoint intervals of the Gencode V35 gene annotation for more than 19 000 GTExV8 BigWig files in approximately 1 h using 32 threads. Megadepth is available both as a command-line tool and as an R/Bioconductor package providing much faster quantification compared to the rtracklayer package.

Availability and implementation
https://github.com/ChristopherWilks/megadepth, https://bioconductor.org/packages/megadepth.

Supplementary information
Supplementary data are available at Bioinformatics online.
SP  - 3014
IS  - 18
VL  - 37
PB  - OXFORD UNIV PRESS
JF  - Bioinformatics
N1  - This work is licensed under a Creative Commons Attribution 4.0 International License. The images
or other third-party material in this article are included in the Creative Commons license,
unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license,
users will need to obtain permission from the license holder to reproduce the material. To view a copy of this
license, visit http://creativecommons.org/licenses/by/4.0/
EP  - 3016
ID  - discovery10141401
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