Jul 9, 2026 · Download SAM tools for free. SAM (Sequence Alignment/Map) is a flexible generic format for storing nucleotide sequence alignment. SAMtools provide efficient utilities on manipulating alignments in the SAM format.
SAMtools is a toolkit for manipulating alignments in SAM/BAM format, including sorting, merging, indexing and generating alignments in a per-position format (Danecek et al. 2021).