ArticleGigaScience2021
HTSlib: C library for reading/writing high-throughput sequencing data.
Article in GigaScience, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 277 papers, 1 of them a synthesis that pooled it.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
277 citing papers in PubMed, 1 synthesis or guideline pooled it.
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- Genetic dissection of grain yield and correlated proxy traits under suboptimal conditions.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Article
- Long-read based detection of large copy number variants with potential functional significance using the ContextSV structural variant caller.NAR genomics and bioinformatics · 2026Article
- AdmixLD: fast genome-scale inference of ancestry disequilibrium in hybrid zones.Bioinformatics (Oxford, England) · 2026Article
- Two Faces of UV Mutagenesis: Independent and Collateral Mutagenesis in Skin Cancers.Life (Basel, Switzerland) · 2026Article
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- SNPio: a Python interface for population genomic data processing.BMC bioinformatics · 2026Article
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- Restriction-modification systems are required forProceedings of the National Academy of Sciences of the United States of America · 2026Article
- Chromosome-Level Genome Assembly of the Sea Urchin Glyptocidaris crenularis and Sex Chromosome Identification.Biochemical genetics · 2026Article
- A stratified urine-based molecular diagnostic and prognostic model for non-muscle-invasive bladder cancer management.BMC cancer · 2026Article
- HyDRA: A pipeline for integrating long- and short-read RNAseq data for custom transcriptome assembly.iScience · 2026Article
- ScriptManager: a platform for scalable and reproducible high-resolution analysis of genomics datasets.bioRxiv : the preprint server for biology · 2026Article
217 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
8 authors.
Funding
Abstract
backgroundSince 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.
findingsWe 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 iterators, and better use of threading.
conclusionSince the original Samtools release, performance has been considerably improved, with a BAM read-write loop running 5 times faster and BAM to SAM conversion 13 times faster (both using 16 threads, compared to Samtools 0.1.19). Widespread adoption has seen HTSlib downloaded >1 million times from GitHub and conda. The C library has been used directly by an estimated 900 GitHub projects and has been incorporated into Perl, Python, Rust, and R, significantly expanding the number of uses via other languages. HTSlib is open source and is freely available from htslib.org under MIT/BSD license.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.