Sequence Alignment/Map format: a comprehensive review of approaches and applications

Yuansheng Liu; Xiangzhen Shen; Yongshun Gong; Yiping Liu; Bosheng Song; Xiangxiang Zeng

doi:10.1093/bib/bbad320

Sequence Alignment/Map format: a comprehensive review of approaches and applications

Brief Bioinform. 2023 Sep 20;24(5):bbad320. doi: 10.1093/bib/bbad320.

Authors

Yuansheng Liu¹, Xiangzhen Shen¹, Yongshun Gong², Yiping Liu¹, Bosheng Song¹, Xiangxiang Zeng¹

Affiliations

¹ College of Computer Science and Electronic Engineering, Hunan University, 410086, Changsha, China.
² School of Software, Shandong University, 250100, Jinan, China.

PMID: 37668049
DOI: 10.1093/bib/bbad320

Abstract

The Sequence Alignment/Map (SAM) format file is the text file used to record alignment information. Alignment is the core of sequencing analysis, and downstream tasks accept mapping results for further processing. Given the rapid development of the sequencing industry today, a comprehensive understanding of the SAM format and related tools is necessary to meet the challenges of data processing and analysis. This paper is devoted to retrieving knowledge in the broad field of SAM. First, the format of SAM is introduced to understand the overall process of the sequencing analysis. Then, existing work is systematically classified in accordance with generation, compression and application, and the involved SAM tools are specifically mined. Lastly, a summary and some thoughts on future directions are provided.

Keywords: SAM format; The Sequence Alignment/Map format; sequence alignment; sequence analysis.

Publication types

Review
Research Support, Non-U.S. Gov't

MeSH terms

Sequence Alignment*