SAM/BAM format v1.5 extensions forde novoassemblies

• DOI: 10.1101/020024
• Publication Date: 2015-05-30T06:13:25Z
• Authors: Peter J. A. Cock; James Bonfield; Bastien Chevreux; Heng Li
• Keywords: Sequence (biology); File format; k-mer

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