A team led by (now graduated) Ph.D. student Chris Wilks published a new study in the journal Bioinformatics describing the software tool Megadepth.  Megadepth is a fast tool for quantifying alignments and coverage for BigWig and BAM/CRAM input files — i.e. summing or averaging the depth of coverage over genomic intervals.  It uses 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 hour using 32 threads.

Importantly, Megadepth is available both as a command-line tool and as an R/Bioconductor package.  The R/Bioconductor package provides much faster quantification compared to the existing rtracklayer package.

The Megadepth software is available via Bioconda and Bioconductor.  The MIT-licensed source code is available at https://github.com/ChristopherWilks/megadepth.

Huge congratulations to the team! – including Chris, Omar, Daniel, Leonardo Collado-Torres of the Lieber Institute for Brain Development, and David Zhang of University College London.