biobambam: tools for read pair collation based algorithms on BAM files

TL;DR

biobambam is a set of tools and an API designed for efficient processing of BAM files, enabling read pair collation and supporting tasks like duplicate marking and FastQ conversion more efficiently than previous methods.

Contribution

introduction of biobambam, an API and tools for efficient read pair collation in BAM files without full resorting, improving performance over existing solutions.

Findings

faster processing of BAM files for duplicate marking

more memory-efficient than previous tools

enables faster FastQ conversion

Abstract

Sequence alignment data is often ordered by coordinate (id of the reference sequence plus position on the sequence where the fragment was mapped) when stored in BAM files, as this simplifies the extraction of variants between the mapped data and the reference or of variants within the mapped data. In this order paired reads are usually separated in the file, which complicates some other applications like duplicate marking or conversion to the FastQ format which require to access the full information of the pairs. In this paper we introduce biobambam, an API for efficient BAM file reading supporting the efficient collation of alignments by read name without performing a complete resorting of the input file and some tools based on this API performing tasks like marking duplicate reads and conversion to the FastQ format. In comparison with previous approaches to problems involving the collation of alignments by read name like the BAM to FastQ or duplication marking utilities in the Picard suite the approach of biobambam can often perform an equivalent task more efficiently in terms of the required main memory and run-time.