rust-bio/rust-htslib: This library provides HTSlib bindings and a high level Rust API for reading and writing BAM files. github.com/rust-bio/rus...
GitHub - rust-bio/rust-htslib: This library provides HTSlib bindings and a high level Rust API for reading and writing BAM files.
This library provides HTSlib bindings and a high level Rust API for reading and writing BAM files. - rust-bio/rust-htslib
github.com
February 27, 2026 at 11:24 AM
rust-bio/rust-htslib: This library provides HTSlib bindings and a high level Rust API for reading and writing BAM files. github.com/rust-bio/rus...
Release 1.22 of HTSlib, SAMtools, and BCFtools is now available from GitHub. See htslib.org/download/ for links to tarballs and release notes. 🧪
#samtools #bcftools #htslib #bioinformatics
#samtools #bcftools #htslib #bioinformatics
Samtools
Samtools
htslib.org
May 30, 2025 at 10:22 AM
Release 1.22 of HTSlib, SAMtools, and BCFtools is now available from GitHub. See htslib.org/download/ for links to tarballs and release notes. 🧪
#samtools #bcftools #htslib #bioinformatics
#samtools #bcftools #htslib #bioinformatics
I've just released #rust-htslib 1.0. After a long time with a pretty stable API usage of rust-htslib in production, it feels like the right time to finally move to 1.0. Most important change is probably a switch to thread-safe pointers in BAM record handling. github.com/rust-bio/rus...
January 29, 2026 at 10:37 AM
I've just released #rust-htslib 1.0. After a long time with a pretty stable API usage of rust-htslib in production, it feels like the right time to finally move to 1.0. Most important change is probably a switch to thread-safe pointers in BAM record handling. github.com/rust-bio/rus...
New paper from my lab! QPL-HTSLib, an integration of HTSLib with Intel's QPL for speedups of 10x for BAM compression and 1.4x for BAM decompression on QPL-compatible Intel CPUs doi.org/10.1093/bioa...
Validate User
doi.org
August 26, 2026 at 11:39 PM
New paper from my lab! QPL-HTSLib, an integration of HTSLib with Intel's QPL for speedups of 10x for BAM compression and 1.4x for BAM decompression on QPL-compatible Intel CPUs doi.org/10.1093/bioa...
SAMtools / HTSLib / BCFTools 1.23 has been released. See the releasenotes on GitHub and www.htslib.org for details.
Samtools
Samtools
www.htslib.org
December 16, 2025 at 3:33 PM
SAMtools / HTSLib / BCFTools 1.23 has been released. See the releasenotes on GitHub and www.htslib.org for details.
Release 1.24 of HTSlib, SAMtools, and BCFtools is now available from GitHub. See htslib.org/download/ for links to tarballs and release notes.
🧪🧬🖥️
🧪🧬🖥️
Samtools
Samtools
htslib.org
July 9, 2026 at 3:13 PM
Release 1.24 of HTSlib, SAMtools, and BCFtools is now available from GitHub. See htslib.org/download/ for links to tarballs and release notes.
🧪🧬🖥️
🧪🧬🖥️
A reminder to SAMtools / HTSlib users, from the next release (probably April 2025) CRAM 3.1 will be the default version used. Use "samtools view -O cram,version=3.0" to switch back to the current 3.0.
(But note 3.1 should be smaller and faster, especially on Illumina.)
(But note 3.1 should be smaller and faster, especially on Illumina.)
March 26, 2025 at 11:14 PM
A reminder to SAMtools / HTSlib users, from the next release (probably April 2025) CRAM 3.1 will be the default version used. Use "samtools view -O cram,version=3.0" to switch back to the current 3.0.
(But note 3.1 should be smaller and faster, especially on Illumina.)
(But note 3.1 should be smaller and faster, especially on Illumina.)
I spent some time writing about a #rust library I've been working on: seqair, an alternative to (a subset of) htslib. This is a big one! So much potential API surface to cover and I better have a good reason for it! deterministic.space/seqair.html
Seqair, my Rust-native take on htslib
This post introduces seqair , a new Rust library for bioinformatics formats I’ve been working on. We’ll look in detail at one of my main design choices here, a columnar store for iterating BAM data, …
deterministic.space
April 30, 2026 at 5:47 PM
I spent some time writing about a #rust library I've been working on: seqair, an alternative to (a subset of) htslib. This is a big one! So much potential API surface to cover and I better have a good reason for it! deterministic.space/seqair.html
Note with the new release (1.24) of samtools / bcftools / htslib, we took the decision to drop CRAM 4.0 support. This is because htslib was the only thing that implemented it AFAIK, it was an experimental prerelease and not an adopted standard, and sadly it wasn't as well engineered as it should be
July 9, 2026 at 3:21 PM
Note with the new release (1.24) of samtools / bcftools / htslib, we took the decision to drop CRAM 4.0 support. This is because htslib was the only thing that implemented it AFAIK, it was an experimental prerelease and not an adopted standard, and sadly it wasn't as well engineered as it should be
For those working with Hi-C data and the Arima workflow, we have rewritten the Arima tools using htslib to speed up the process. Any feedback is welcome: github.com/Genoscope-LB...
February 14, 2025 at 4:24 PM
For those working with Hi-C data and the Arima workflow, we have rewritten the Arima tools using htslib to speed up the process. Any feedback is welcome: github.com/Genoscope-LB...
Maybe the fastest BCF/VCF to #RStats DataFrames using #htslib and #duckdb C API. Easily the title of fastest BCF/VCF to parquet convertors in #RStats (no other R options :D). This was motivated, among other things, by the idea of trying out #DuckLake in a familiar field
github.com/RGenomicsETL...
github.com/RGenomicsETL...
January 19, 2026 at 8:27 PM
a post about how, with LLMs, I wrote a new set of libraries.
Wrapping htslib is my hello-world but doing it in rust to allow javascript expressions handled by V8 was more substantial project.
The tools and LLMs are now getting quite good:
brentp.github.io/latest/blog/...
let me know what you think
Wrapping htslib is my hello-world but doing it in rust to allow javascript expressions handled by V8 was more substantial project.
The tools and LLMs are now getting quite good:
brentp.github.io/latest/blog/...
let me know what you think
AI Coding - Brent Pedersen
Writing real software with AI coding tools
brentp.github.io
December 30, 2025 at 4:42 PM
a post about how, with LLMs, I wrote a new set of libraries.
Wrapping htslib is my hello-world but doing it in rust to allow javascript expressions handled by V8 was more substantial project.
The tools and LLMs are now getting quite good:
brentp.github.io/latest/blog/...
let me know what you think
Wrapping htslib is my hello-world but doing it in rust to allow javascript expressions handled by V8 was more substantial project.
The tools and LLMs are now getting quite good:
brentp.github.io/latest/blog/...
let me know what you think
In vg we are vendoring in htslib partly so we can make sure we use an htslib built with libdeflate support. For blocked-gzip at least you can stream the overall file just fine.
January 20, 2026 at 5:24 PM
In vg we are vendoring in htslib partly so we can make sure we use an htslib built with libdeflate support. For blocked-gzip at least you can stream the overall file just fine.
Release 1.22 of HTSlib, SAMtools, and BCFtools is now available from GitHub. See htslib.org/download/ for links to tarballs and release notes.
Samtools
Samtools
htslib.org
May 31, 2025 at 7:49 AM
Release 1.22 of HTSlib, SAMtools, and BCFtools is now available from GitHub. See htslib.org/download/ for links to tarballs and release notes.
Today's pysam 0.24.0 release bundles htslib, samtools, and bcftools 1.23.1 and has pre-built wheels for Python 3.8 through 3.14. Notably it includes modified_bases fixes thanks to reports by Leszek Pryszcz and Jun Mencius, and new documentation for VariantRecord et al written by @timd.one. 🧬🖥️
Release v0.24.0 · pysam-developers/pysam
This pysam release wraps htslib/samtools/bcftools version 1.23.1 (PR #1343, PR #1372, and PR #1396) and now requires Cython 3.
It has been tested with Python versions 3.8 through 3.14, and wheels a...
github.com
April 27, 2026 at 12:31 PM
Today's pysam 0.24.0 release bundles htslib, samtools, and bcftools 1.23.1 and has pre-built wheels for Python 3.8 through 3.14. Notably it includes modified_bases fixes thanks to reports by Leszek Pryszcz and Jun Mencius, and new documentation for VariantRecord et al written by @timd.one. 🧬🖥️
#Duckdb #htslib #Genomics #Bioinformatics #RStats
duckths: Read HTS (VCF/BCF/BAM/CRAM/FASTA/FASTQ/GTF/GFF) files in DuckDB via htslib
Rduckhts: 'DuckDB' High Throughput Sequencing File Formats Reader Extension
genomic.social/@bioinfhotep...
duckths: Read HTS (VCF/BCF/BAM/CRAM/FASTA/FASTQ/GTF/GFF) files in DuckDB via htslib
Rduckhts: 'DuckDB' High Throughput Sequencing File Formats Reader Extension
genomic.social/@bioinfhotep...
SMT (@bioinfhotep@genomic.social)
Attached: 4 images
#Genomics #Bioinformatics
Release of duckhts: #htslib based #Duckdb Extension for High Throughput Sequencing File Formats
https://duckdb.org/community_extensions/extensions/duckh...
genomic.social
February 21, 2026 at 11:04 PM
#Duckdb #htslib #Genomics #Bioinformatics #RStats
duckths: Read HTS (VCF/BCF/BAM/CRAM/FASTA/FASTQ/GTF/GFF) files in DuckDB via htslib
Rduckhts: 'DuckDB' High Throughput Sequencing File Formats Reader Extension
genomic.social/@bioinfhotep...
duckths: Read HTS (VCF/BCF/BAM/CRAM/FASTA/FASTQ/GTF/GFF) files in DuckDB via htslib
Rduckhts: 'DuckDB' High Throughput Sequencing File Formats Reader Extension
genomic.social/@bioinfhotep...
Second post about Seqair, my #rustlang take on htslib. This one is about streaming VCF/BCF writing and type-state/session type APIs! #bioinformatics
Using Rust typestates for BCF writing
Using Rust typestates for BCF writing
deterministic.space
May 8, 2026 at 10:44 AM
Second post about Seqair, my #rustlang take on htslib. This one is about streaming VCF/BCF writing and type-state/session type APIs! #bioinformatics
📚 New paper in Bioinformatics Advances: "QPL-enabled HTSlib library: Accelerating sequence file compression using Intel IAA"
Read more: https://doi.org/10.1093/bioadv/vbag250
Authors include: @niema.net
Read more: https://doi.org/10.1093/bioadv/vbag250
Authors include: @niema.net
September 9, 2026 at 12:01 PM
📚 New paper in Bioinformatics Advances: "QPL-enabled HTSlib library: Accelerating sequence file compression using Intel IAA"
Read more: https://doi.org/10.1093/bioadv/vbag250
Authors include: @niema.net
Read more: https://doi.org/10.1093/bioadv/vbag250
Authors include: @niema.net
From time to time, trivial incidental details are key to understanding a bug report. This is an excellent example: if the reporter had not happened to include part of their shell prompt in their transcript of the build failure, this would have been extremely mysterious. github.com/samtools/hts...
HTSLIB make command during installation · Issue #1904 · samtools/htslib
Hello! Has anyone encountered the issue make: *** [Makefile:730: htslib-uninstalled.pc] Error 1 when installing HTSLIB? I have tried the steps in the xSqueezeIt repository and it worked on 2 differ...
github.com
April 3, 2025 at 10:08 PM
From time to time, trivial incidental details are key to understanding a bug report. This is an excellent example: if the reporter had not happened to include part of their shell prompt in their transcript of the build failure, this would have been extremely mysterious. github.com/samtools/hts...
This is the work of @killercup.de - a lot of careful engineering went into this. Seems to pass most (if not all?) htslib tests. The other benefit is that it removes dynamic link dependencies introduced by rust-htslib
July 17, 2026 at 10:15 AM
This is the work of @killercup.de - a lot of careful engineering went into this. Seems to pass most (if not all?) htslib tests. The other benefit is that it removes dynamic link dependencies introduced by rust-htslib
🎉See C versions of Arima Genomics mapping pipeline tools (htslib library). These tools are designed to efficiently process & analyze HTS sequencing data, particularly for Hi-C & other chromosome conformation capture experiments.
github.com/Genoscope-LBGB/arima_htslib
#bioinformatic #genomic #Hi-C
github.com/Genoscope-LBGB/arima_htslib
#bioinformatic #genomic #Hi-C
February 17, 2025 at 11:20 PM
🎉See C versions of Arima Genomics mapping pipeline tools (htslib library). These tools are designed to efficiently process & analyze HTS sequencing data, particularly for Hi-C & other chromosome conformation capture experiments.
github.com/Genoscope-LBGB/arima_htslib
#bioinformatic #genomic #Hi-C
github.com/Genoscope-LBGB/arima_htslib
#bioinformatic #genomic #Hi-C
The htslib.org web site for samtools/htslib/bcftools, or generally get source code from the respective (mostly) GitHub repositories. Build binaries yourself or get them from relatively trusted sources like Linux distributions, brew, or bioconda.
Samtools
Samtools
htslib.org
September 15, 2025 at 12:24 PM
The htslib.org web site for samtools/htslib/bcftools, or generally get source code from the respective (mostly) GitHub repositories. Build binaries yourself or get them from relatively trusted sources like Linux distributions, brew, or bioconda.
HTSlib also has APIs for parsing MM & ML values. They're accessible via pysam (AlignedSegment's modified_bases property) and test/test_mod is a test harness in the HTSlib repo or tarball that takes a SAM/BAM/CRAM file and dumps out its view of the modified bases in a fairly human-readable format.
July 17, 2025 at 8:58 PM
HTSlib also has APIs for parsing MM & ML values. They're accessible via pysam (AlignedSegment's modified_bases property) and test/test_mod is a test harness in the HTSlib repo or tarball that takes a SAM/BAM/CRAM file and dumps out its view of the modified bases in a fairly human-readable format.
New Samtools, Htslib and Bcftools 1.19 releases available.
github.com/samtools/sam... and co.
#bioinformatics 🧪
github.com/samtools/sam... and co.
#bioinformatics 🧪
December 12, 2023 at 4:22 PM
New Samtools, Htslib and Bcftools 1.19 releases available.
github.com/samtools/sam... and co.
#bioinformatics 🧪
github.com/samtools/sam... and co.
#bioinformatics 🧪
That meant that a number of the recent CVEs were related to the complexity of CRAM 4.0 encodings. While we fixed all we found, it seemed a poor trade off for something that's totally unused. Htslib without 4.0 is simply more battle-hardened.
(3.1 is still the default)
(3.1 is still the default)
July 9, 2026 at 3:23 PM
That meant that a number of the recent CVEs were related to the complexity of CRAM 4.0 encodings. While we fixed all we found, it seemed a poor trade off for something that's totally unused. Htslib without 4.0 is simply more battle-hardened.
(3.1 is still the default)
(3.1 is still the default)