BamToCov: an efficient toolkit for sequence coverage calculations

Abstract

Many genomics applications requires the calculation of nucleotide coverage of a reference or counting how many reads maps in a reference region. Here we present BamToCov, a suite of tools for rapid and flexible coverage calculations relying on a memory efficient algorithm and designed for flexible integration in bespoke pipelines. The tools of the suite will process sorted BAM or CRAM files, allowing to extract coverage information using different filtering approaches. BamToCov tools, unlike existing tools already available, have been developed to require a minimum amount of memory, to be easily integrated in workflows, and to allow for strand-specific coverage analyses. The unique coverage calculation algorithm makes it the ideal choice for the analysis of long reads alignments. The programs and their documentation are freely available at https://github.com/telatin/bamtocov.