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.

References:

• Wilks, C, Ahmed, O, Baker, DN, Zhang, D, Collado-Torres, L, Langmead, B (2021).
  Megadepth: efficient coverage quantification for BigWigs and BAMs.
  Bioinformatics,

• MEGADEPTH Home page

• Module Name: megadepth (see the modules page for more information)
• Unusual environment variables set

Allocate an interactive session and run the program. Sample session:

[user@biowulf]$ sinteractive --mem=20g -n 14
[user@cn3316 ~]$ module load megadepth
[+] Loading megadepth  1.2.0
[user@cn3316 ~]$ megadepth
megadepth 1.2.0

BAM and BigWig utility.

Usage:
  megadepth  [options]

Options:
  -h --help                Show this screen.
  --version                Show version.
  --threads                # of threads to do: BAM decompression OR compute sums over multiple BigWigs in parallel
                            if the 2nd is intended then a TXT file listing the paths to the BigWigs to process in parallel
                            should be passed in as the main input file instead of a single BigWig file (EXPERIMENTAL).
  --prefix                 String to use to prefix all output files.
  --no-auc-stdout          Force all AUC(s) to be written to .auc.tsv rather than STDOUT
  --no-annotation-stdout   Force summarized annotation regions to be written to .annotation.tsv rather than STDOUT
  --no-coverage-stdout     Force covered regions to be written to .coverage.tsv rather than STDOUT
  --keep-order             Output annotation coverage in the order chromosomes appear in the BAM/BigWig file
                           The default is to output annotation coverage in the order chromosomes appear in the annotation BED file.
                           This is only applicable if --annotation is used for either BAM or BigWig input.

[user@cn3316 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$