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Related Experiment Video

Updated: Nov 17, 2025

High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture 4C-seq

High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture 4C-seq

Published on: October 5, 2018

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

James K Bonfield¹, John Marshall², Petr Danecek¹

¹Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK.

|February 17, 2021

Summary

This summary is machine-generated.

A new software library, HTSlib, offers improved access to sequencing data formats like VCF and SAM. It enhances performance and robustness, supporting genomic data analysis and international standards.

Keywords:

bcftools data analysis high-throughput sequencing next generation sequencing samtools variant calling

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Area of Science:

Genomics
Bioinformatics
Computational Biology

Background:

The VCF (Variant Call Format) and SAM (Sequence Alignment Map) file formats are foundational in genomics.
Numerous software tools have been developed for processing these data files.
HTSlib originated from the SAMtools implementation, focusing on performance and robustness.

Purpose of the Study:

To present a software library for programmatic access to sequencing alignment and variant data formats.
To introduce improvements and new features over the original SAMtools and BCFtools applications.

Main Methods:

Development of a C library providing programmatic access to sequencing alignment and variant formats.
Incorporation of newer access protocols, CRAM file format support, enhanced indexing and iterators, and improved threading.
Building upon the established SAMtools and BCFtools codebases.

Main Results:

Significant performance improvements, including a 5x faster BAM read-write loop and a 13x faster BAM to SAM conversion using 16 threads.
Widespread adoption with over 1 million downloads from GitHub and conda.
Integration into approximately 900 GitHub projects and multiple programming languages (Perl, Python, Rust, R).

Conclusions:

HTSlib offers a robust and performant solution for accessing genomic data formats.
Its widespread adoption and integration into various programming languages highlight its utility and impact.
The library is open-source, freely available under the MIT/BSD license, promoting further development and application.