Heads up: ignore samtools dot org, similarly minimap2 dot com and likely others. It's owned by a known phishing site and while the binaries they offer look valid currently (but note they may be serving us different binaries to others), that could change.
Ie: it's not us (Samtools team)! Be warned
Ie: it's not us (Samtools team)! Be warned
September 15, 2025 at 8:40 AM
Heads up: ignore samtools dot org, similarly minimap2 dot com and likely others. It's owned by a known phishing site and while the binaries they offer look valid currently (but note they may be serving us different binaries to others), that could change.
Ie: it's not us (Samtools team)! Be warned
Ie: it's not us (Samtools team)! Be warned
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
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.)
Initial version running Minimap2, Samtools, and ViralConsensus is complete, built completely from scratch! Constructed a consensus HIV-1 genome sequence 30X-coverage paired-end reads on a Gameboy-looking handheld gaming device 😂 youtu.be/Mvflrp2-npA
Running Minimap2, Samtools, and ViralConsensus on an R36S game console
YouTube video by Niema Moshiri
youtu.be
December 23, 2024 at 11:54 PM
Initial version running Minimap2, Samtools, and ViralConsensus is complete, built completely from scratch! Constructed a consensus HIV-1 genome sequence 30X-coverage paired-end reads on a Gameboy-looking handheld gaming device 😂 youtu.be/Mvflrp2-npA
You mean this from samtools dot org is not a human-made graph?
September 15, 2025 at 1:26 PM
You mean this from samtools dot org is not a human-made graph?
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.
🧵 How to Use samtools – A Must-Know Tool for NGS Data
If you're working with sequencing data, samtools is essential. It was developed by Heng Li, who also created BWA and minimap2. Let's dive into its usage. 👇
If you're working with sequencing data, samtools is essential. It was developed by Heng Li, who also created BWA and minimap2. Let's dive into its usage. 👇
February 4, 2025 at 2:45 PM
🧵 How to Use samtools – A Must-Know Tool for NGS Data
If you're working with sequencing data, samtools is essential. It was developed by Heng Li, who also created BWA and minimap2. Let's dive into its usage. 👇
If you're working with sequencing data, samtools is essential. It was developed by Heng Li, who also created BWA and minimap2. Let's dive into its usage. 👇
One time I found a bug in samtools and it was only confirmed cause I tweeted about it
June 4, 2025 at 9:18 AM
One time I found a bug in samtools and it was only confirmed cause I tweeted about it
I asked ChatGPT questions about bwa and samtools. The answer it gave me, regarding both programs, were super wrong. And these are like bread-and-butter bioinformatics programs.
It's just so much better to pull out `-help` than trying to ask LLM. What a waste of energy and time.
It's just so much better to pull out `-help` than trying to ask LLM. What a waste of energy and time.
June 18, 2025 at 1:19 PM
I asked ChatGPT questions about bwa and samtools. The answer it gave me, regarding both programs, were super wrong. And these are like bread-and-butter bioinformatics programs.
It's just so much better to pull out `-help` than trying to ask LLM. What a waste of energy and time.
It's just so much better to pull out `-help` than trying to ask LLM. What a waste of energy and time.
If you use fgbio or UMIs at all, you should start using fgumi. Up to 100x faster, and soon 2x faster sort than samtools, it’s been a labor of love and something we’ve wanted to do for a long time.
March 31, 2026 at 3:56 PM
If you use fgbio or UMIs at all, you should start using fgumi. Up to 100x faster, and soon 2x faster sort than samtools, it’s been a labor of love and something we’ve wanted to do for a long time.
Release 1.23.1 of HTSlib, SAMtools, and BCFtools is now available from GitHub. This fixes crashes that could occur when reading malformed CRAM or GZI files. See htslib.org/download/ for links to tarballs and release notes.
🧪🧬🖥️
#samtools #bioinformatics #genomics
🧪🧬🖥️
#samtools #bioinformatics #genomics
Samtools
Samtools
htslib.org
March 18, 2026 at 5:16 PM
Release 1.23.1 of HTSlib, SAMtools, and BCFtools is now available from GitHub. This fixes crashes that could occur when reading malformed CRAM or GZI files. See htslib.org/download/ for links to tarballs and release notes.
🧪🧬🖥️
#samtools #bioinformatics #genomics
🧪🧬🖥️
#samtools #bioinformatics #genomics
Spending a nice Sunday afternoon in my quiet lab installing and testing informatics programs on our beast computers, and thinking back to when I first started coding and had no idea what I was doing. I think I remember it taking 4 days for me to install samtools right 🤣
March 15, 2026 at 10:40 PM
Spending a nice Sunday afternoon in my quiet lab installing and testing informatics programs on our beast computers, and thinking back to when I first started coding and had no idea what I was doing. I think I remember it taking 4 days for me to install samtools right 🤣
Samtools is the best bioinformatics tool named after a guy called Sam
March 25, 2025 at 6:21 PM
Samtools is the best bioinformatics tool named after a guy called Sam
Introducing RustQC: 60x faster RNA-Seq quality control!
We used AI to reimplement 15 RNA-Seq QC tools (dupRadar, Qualimap, RSeQC, Preseq, samtools, featureCounts) into a single tool, written in @rust-lang.org:
✅ 15 h analyses → 15 min
✅ Identical outputs
✅ Drastically reduced I/O
We used AI to reimplement 15 RNA-Seq QC tools (dupRadar, Qualimap, RSeQC, Preseq, samtools, featureCounts) into a single tool, written in @rust-lang.org:
✅ 15 h analyses → 15 min
✅ Identical outputs
✅ Drastically reduced I/O
April 2, 2026 at 3:38 PM
Introducing RustQC: 60x faster RNA-Seq quality control!
We used AI to reimplement 15 RNA-Seq QC tools (dupRadar, Qualimap, RSeQC, Preseq, samtools, featureCounts) into a single tool, written in @rust-lang.org:
✅ 15 h analyses → 15 min
✅ Identical outputs
✅ Drastically reduced I/O
We used AI to reimplement 15 RNA-Seq QC tools (dupRadar, Qualimap, RSeQC, Preseq, samtools, featureCounts) into a single tool, written in @rust-lang.org:
✅ 15 h analyses → 15 min
✅ Identical outputs
✅ Drastically reduced I/O
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.
One user had a FASTQ dataset that... Everything aligned to the reference genome fine, but samtools only output ~10 reads into the pile-up file.
Apparently, the quality scores for all the reads were lower than the default filtering used by samtools.
Apparently, the quality scores for all the reads were lower than the default filtering used by samtools.
July 13, 2026 at 8:04 PM
One user had a FASTQ dataset that... Everything aligned to the reference genome fine, but samtools only output ~10 reads into the pile-up file.
Apparently, the quality scores for all the reads were lower than the default filtering used by samtools.
Apparently, the quality scores for all the reads were lower than the default filtering used by samtools.
Yeah but SAMtools is performing much worse than Drcornaned
September 15, 2025 at 2:54 PM
Yeah but SAMtools is performing much worse than Drcornaned
That's why I only write software that can be run on the potatoiest of potatoes 😤 Run bioinformatics workflows in the cloud? Nah fam, I have a $30 Gameboy-looking emulation device 🤌 youtu.be/Mvflrp2-npA?...
Running Minimap2, Samtools, and ViralConsensus on an R36S game console
YouTube video by Niema Moshiri
youtu.be
January 14, 2026 at 5:50 AM
That's why I only write software that can be run on the potatoiest of potatoes 😤 Run bioinformatics workflows in the cloud? Nah fam, I have a $30 Gameboy-looking emulation device 🤌 youtu.be/Mvflrp2-npA?...
TIL that "samtools flagstat" has an option for JSON output and I'm loving it!
October 2, 2023 at 8:42 AM
TIL that "samtools flagstat" has an option for JSON output and I'm loving it!
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 🧪
As a project to learn #Zig, I wrote z-fasta, a drop-in replacement for samtools faidx. It indexes ~17x faster using mmap/SIMD. It's early days, and I have a lot more planned, but I'd really appreciate any feedback or bug reports from the #Bioinformatics community!
github.com/eneskemalerg...
github.com/eneskemalerg...
GitHub - eneskemalergin/z-fasta: ⚡ SIMD-accelerated FASTA indexer written in Zig. 15–17x faster than samtools faidx. mmap, zero dependencies, single binary. Produces byte-identical .fai output.
⚡ SIMD-accelerated FASTA indexer written in Zig. 15–17x faster than samtools faidx. mmap, zero dependencies, single binary. Produces byte-identical .fai output. - eneskemalergin/z-fasta
github.com
March 14, 2026 at 6:39 AM
As a project to learn #Zig, I wrote z-fasta, a drop-in replacement for samtools faidx. It indexes ~17x faster using mmap/SIMD. It's early days, and I have a lot more planned, but I'd really appreciate any feedback or bug reports from the #Bioinformatics community!
github.com/eneskemalerg...
github.com/eneskemalerg...
Two hours of `gatk ValidateSamFile` can save 2 seconds of `samtools quickcheck`, as it turns out.
#bioinformatics
#bioinformatics
November 27, 2024 at 7:46 AM
Two hours of `gatk ValidateSamFile` can save 2 seconds of `samtools quickcheck`, as it turns out.
#bioinformatics
#bioinformatics