SAM/BAM format v1.5 extensions for de novo assemblies

Abstract

SummaryThe plain text Sequence Alignment/Map (SAM) file format and its companion binary form (BAM) are a generic alignment format for storing read alignments against reference sequences (and unmapped reads) together with structured meta-data (Li et al., 2009). Driven by the needs of the 1000 Genomes Project which sequenced many individual human genomes, early SAM/BAM usage focused on pairwise alignments of reads to a reference. However, through the CIGAR P operator multiple sequence alignments can also be preserved. Herein we describe clarifications and additions in version 1.5 of the specification to facilitate storing de novo sequence alignments: Padded reference sequences (with gap characters), annotation of reads or regions of the reference, and the option of embedding the reference sequence within the file.\n\nAvailabilityThe latest public release of the specification is at http://samtools.sourceforge.net/SAM1.pdf, with in development drafts at https://github.com/samtools/hts-specs/ under version control.\n\nContactpeter.cock@hutton.ac.uk