Megadepth: efficient coverage quantification for BigWigs and BAMs

• DOI: 10.1093/bioinformatics/btab152
• Publication Date: 2021-03-04T12:13:12Z
• Authors: Christopher Wilks; Omar Ahmed; Daniel N Baker; David Zhang; Leonardo Collado-...; Ben Langmead
• Keywords: Bioconductor; R package; Disjoint sets; File format

A common way to summarize sequencing datasets is quantify data lying within genes or other genomic intervals. This can be slow and require different tools for input file types.Megadepth a fast tool quantifying alignments coverage BigWig BAM/CRAM files, using substantially less memory than the next-fastest competitor. Megadepth all disjoint intervals of Gencode V35 gene annotation more 19 000 GTExV8 files in approximately 1 h 32 threads. available both as command-line an R/Bioconductor package providing much faster quantification compared rtracklayer package.https://github.com/ChristopherWilks/megadepth, https://bioconductor.org/packages/megadepth.Supplementary are at Bioinformatics online.