Tools to extract coverage informations from BAM (and CRAM) files, based on the covtobed algorithm that supports stranded coverage and physical coverage, input from streams and uses a memory-efficient algorithm.

Full documentation is available online at the 📖 dedicated website, or in this repository under docs.

The BamToCov package is available from 📦 BioConda

conda install -y -c bioconda bamtocov

Bamtocov has the smallest memory footprint of any other coverage tool, while maintaining reasonable speeds

• Four BAM files used for the benchmarks are available from Zenodo
• A Dockerfile with an automatic speed test is available in this repository

• Brent Pedersen, Aaron Quinlan, hts-nim: scripting high-performance genomic analyses (Bioinformatics)
• Giovanni Birolo, Andrea Telatin, covtobed: a simple and fast tool to extract coverage tracks from BAM files (JOSS)

Initially we also used Lapper, and I recommend checking out this library for fast interval operations.

Giovanni Birolo, Andrea Telatin, BamToCov: an efficient toolkit for sequence coverage calculations, Bioinformatics, 2022