Introduction

SAM (Sequence Alignment/Map) format is a generic format for storing large nucleotide sequence alignments. SAM aims to be a format that:

SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format.

SAMtools is hosted by SourceForge.net. The project page is here. The source code releases are available from the download page. You can check out the most recent source code from the github project page with:


Publication