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 bamtocovBamtocov 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
- Giovanni Birolo, Andrea Telatin BamToCov: an efficient toolkit for sequence coverage calculations (BioRχiv)
- 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.