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Sequence alignment data is often ordered by coordinate (id of the referencesequence plus position on the sequence where the fragment was mapped) whenstored in BAM files, as this simplifies the extraction of variants between themapped data and the reference or of variants within the mapped data. In thisorder paired reads are usually separated in the file, which complicates someother applications like duplicate marking or conversion to the FastQ formatwhich require to access the full information of the pairs. In this paper weintroduce biobambam, an API for efficient BAM file reading supporting theefficient collation of alignments by read name without performing a completeresorting of the input file and some tools based on this API performing taskslike marking duplicate reads and conversion to the FastQ format. In comparisonwith previous approaches to problems involving the collation of alignments byread name like the BAM to FastQ or duplication marking utilities in the Picardsuite the approach of biobambam can often perform an equivalent task moreefficiently in terms of the required main memory and run-time.

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