HTSlib: C library for reading/writing high-throughput sequencing data.

ABSTRACT:

Background

Since the original publication of the VCF and SAM formats, an explosion of software tools have been created to process these data files. To facilitate this a library was produced out of the original SAMtools implementation, with a focus on performance and robustness. The file formats themselves have become international standards under the jurisdiction of the Global Alliance for Genomics and Health.

Findings

We present a software library for providing programmatic access to sequencing alignment and variant formats. It was born out of the widely used SAMtools and BCFtools applications. Considerable improvements have been made to the original code plus many new features including newer access protocols, the addition of the CRAM file format, better indexing and itera

SUBMITTER: Bonfield JK 

PROVIDER: S-EPMC7931820 | biostudies-literature | 2021 Feb

REPOSITORIES: biostudies-literature