SeqFu is a swiss-army knife for FASTA and FASTQ manipulation and can be a very handy tool to build your pipelines!
Learn more: github.com/telatin/seqfu2 [2/2]
Learn more: github.com/telatin/seqfu2 [2/2]
GitHub - telatin/seqfu2: :rocket: seqfu - Sequece Fastx Utilities
:rocket: seqfu - Sequece Fastx Utilities. Contribute to telatin/seqfu2 development by creating an account on GitHub.
github.com
October 3, 2026 at 4:55 PM
SeqFu is a swiss-army knife for FASTA and FASTQ manipulation and can be a very handy tool to build your pipelines!
Learn more: github.com/telatin/seqfu2 [2/2]
Learn more: github.com/telatin/seqfu2 [2/2]
JOB OPPORTUNITIES
⏰Oct 16th
➡️Research fellowship
✅Msc Students, at the time of the start of the contract
✅Knowledge of computational methods, namely FASTQ data processing & QC
✅Analysis of predictive models
👉https://tinyurl.com/279tsmj3
#i3Sjobs
⏰Oct 16th
➡️Research fellowship
✅Msc Students, at the time of the start of the contract
✅Knowledge of computational methods, namely FASTQ data processing & QC
✅Analysis of predictive models
👉https://tinyurl.com/279tsmj3
#i3Sjobs
tinyurl.com
October 1, 2026 at 3:36 PM
JOB OPPORTUNITIES
⏰Oct 16th
➡️Research fellowship
✅Msc Students, at the time of the start of the contract
✅Knowledge of computational methods, namely FASTQ data processing & QC
✅Analysis of predictive models
👉https://tinyurl.com/279tsmj3
#i3Sjobs
⏰Oct 16th
➡️Research fellowship
✅Msc Students, at the time of the start of the contract
✅Knowledge of computational methods, namely FASTQ data processing & QC
✅Analysis of predictive models
👉https://tinyurl.com/279tsmj3
#i3Sjobs
New preprint out by PhD student @madshartmann.bsky.social 🥳
We present SCAR, the perfect tool for assessing the impact of #ancientDNA damage on analyses
Validation tests show how damage massively impacts heterozygosity estimates 😨
Check it out here
www.biorxiv.org/content/10.6...
We present SCAR, the perfect tool for assessing the impact of #ancientDNA damage on analyses
Validation tests show how damage massively impacts heterozygosity estimates 😨
Check it out here
www.biorxiv.org/content/10.6...
SCAR: Controlled mutations, ancient DNA damage, and fragmentation of fasta and fastq sequences
Summary: Controlled modification of sequencing data is important for reproducible benchmarking, particularly when evaluating analyses affected by read fragmentation, divergent reference genomes and an...
www.biorxiv.org
September 30, 2026 at 2:16 PM
New preprint out by PhD student @madshartmann.bsky.social 🥳
We present SCAR, the perfect tool for assessing the impact of #ancientDNA damage on analyses
Validation tests show how damage massively impacts heterozygosity estimates 😨
Check it out here
www.biorxiv.org/content/10.6...
We present SCAR, the perfect tool for assessing the impact of #ancientDNA damage on analyses
Validation tests show how damage massively impacts heterozygosity estimates 😨
Check it out here
www.biorxiv.org/content/10.6...
SCAR: Controlled mutations, ancient DNA damage, and fragmentation of fasta and fastq sequences https://www.biorxiv.org/content/10.64898/2026.09.24.754018v1
September 29, 2026 at 9:31 PM
SCAR: Controlled mutations, ancient DNA damage, and fragmentation of fasta and fastq sequences https://www.biorxiv.org/content/10.64898/2026.09.24.754018v1
SCAR: Controlled mutations, ancient DNA damage, and fragmentation of fasta and fastq sequences https://www.biorxiv.org/content/10.64898/2026.09.24.754018v1
September 29, 2026 at 9:31 PM
SCAR: Controlled mutations, ancient DNA damage, and fragmentation of fasta and fastq sequences https://www.biorxiv.org/content/10.64898/2026.09.24.754018v1
I am hiring a postdoc! Are you interested to work on population genetics/ drug resistance/ data? Want to work in Montpellier, France? Fastq files don't scare you?
PhD required, start date hopefully Nov 1! (end date Sep 30 2028)
Please share!
abetterscientist.wordpress.com/2026/09/29/p...
PhD required, start date hopefully Nov 1! (end date Sep 30 2028)
Please share!
abetterscientist.wordpress.com/2026/09/29/p...
Postdoc position on drug resistance evolution in Montpellier, France
I have some exciting news (again!). I got money from the region (Occitanie) to hire a postdoc (and later an engineer / technician) to work on drug resistance evolution in malaria (P. faciparum) and…
abetterscientist.wordpress.com
September 29, 2026 at 3:37 PM
I am hiring a postdoc! Are you interested to work on population genetics/ drug resistance/ data? Want to work in Montpellier, France? Fastq files don't scare you?
PhD required, start date hopefully Nov 1! (end date Sep 30 2028)
Please share!
abetterscientist.wordpress.com/2026/09/29/p...
PhD required, start date hopefully Nov 1! (end date Sep 30 2028)
Please share!
abetterscientist.wordpress.com/2026/09/29/p...
STOP GIVING FILE NAMES SUFFIXES
YEARS OF FILE EXTENSIONS yet NO REAL WORLD USE FIND for anything except .txt
".py" ".cpp" ".fastq" - statements dreamed up by the utterly deranged.
"Hello I'd like to open pdf please"
THEY HAVE PLAYED US FOR ABSOLUTE FOOLS
YEARS OF FILE EXTENSIONS yet NO REAL WORLD USE FIND for anything except .txt
".py" ".cpp" ".fastq" - statements dreamed up by the utterly deranged.
"Hello I'd like to open pdf please"
THEY HAVE PLAYED US FOR ABSOLUTE FOOLS
September 28, 2026 at 8:02 PM
STOP GIVING FILE NAMES SUFFIXES
YEARS OF FILE EXTENSIONS yet NO REAL WORLD USE FIND for anything except .txt
".py" ".cpp" ".fastq" - statements dreamed up by the utterly deranged.
"Hello I'd like to open pdf please"
THEY HAVE PLAYED US FOR ABSOLUTE FOOLS
YEARS OF FILE EXTENSIONS yet NO REAL WORLD USE FIND for anything except .txt
".py" ".cpp" ".fastq" - statements dreamed up by the utterly deranged.
"Hello I'd like to open pdf please"
THEY HAVE PLAYED US FOR ABSOLUTE FOOLS
New release of chelae over the weekend. The fastest adapter and qual trimming software you've probably never heard of 😉
Still measures the fastest of the bunch, though AdapterRemoval v3 isn't too far behind.
Now with support for streaming interleaved FASTQ!
🧬 🖥️
github.com/fulcrumgenom...
Still measures the fastest of the bunch, though AdapterRemoval v3 isn't too far behind.
Now with support for streaming interleaved FASTQ!
🧬 🖥️
github.com/fulcrumgenom...
GitHub - fulcrumgenomics/chelae: Fast, highly accurate, read-trimming for NGS data.
Fast, highly accurate, read-trimming for NGS data. - fulcrumgenomics/chelae
github.com
September 28, 2026 at 5:18 PM
New release of chelae over the weekend. The fastest adapter and qual trimming software you've probably never heard of 😉
Still measures the fastest of the bunch, though AdapterRemoval v3 isn't too far behind.
Now with support for streaming interleaved FASTQ!
🧬 🖥️
github.com/fulcrumgenom...
Still measures the fastest of the bunch, though AdapterRemoval v3 isn't too far behind.
Now with support for streaming interleaved FASTQ!
🧬 🖥️
github.com/fulcrumgenom...
Would you like to inspect FASTQ files from your terminal?
`seqfu less` can do that! You can scroll, search for motives and see intuitive colored bars representing quality values.
Check it out here: telatin.github.io/seqfu2/tools...
`seqfu less` can do that! You can scroll, search for motives and see intuitive colored bars representing quality values.
Check it out here: telatin.github.io/seqfu2/tools...
September 26, 2026 at 4:55 PM
Would you like to inspect FASTQ files from your terminal?
`seqfu less` can do that! You can scroll, search for motives and see intuitive colored bars representing quality values.
Check it out here: telatin.github.io/seqfu2/tools...
`seqfu less` can do that! You can scroll, search for motives and see intuitive colored bars representing quality values.
Check it out here: telatin.github.io/seqfu2/tools...
🦀 Rust is coming for bioinformatics.
Meet Cleaver-X — one binary for:
✂️ Trimming + QC
🧬 FASTA/FASTQ/SAM/BAM
📊 Counting + demux
⚡ Constant-memory streaming
180 MB in 0.17 sec. ~7 MB RAM.
No Python. No C/C++.
Just Rust. 🦀
#Rust #rustsky
Crates
crates.io/crates/Cleav...
Meet Cleaver-X — one binary for:
✂️ Trimming + QC
🧬 FASTA/FASTQ/SAM/BAM
📊 Counting + demux
⚡ Constant-memory streaming
180 MB in 0.17 sec. ~7 MB RAM.
No Python. No C/C++.
Just Rust. 🦀
#Rust #rustsky
Crates
crates.io/crates/Cleav...
crates.io: Rust Package Registry
crates.io serves as a central registry for sharing crates, which are packages or libraries written in Rust that you can use to enhance your projects
crates.io
September 26, 2026 at 4:55 AM
🦀 Rust is coming for bioinformatics.
Meet Cleaver-X — one binary for:
✂️ Trimming + QC
🧬 FASTA/FASTQ/SAM/BAM
📊 Counting + demux
⚡ Constant-memory streaming
180 MB in 0.17 sec. ~7 MB RAM.
No Python. No C/C++.
Just Rust. 🦀
#Rust #rustsky
Crates
crates.io/crates/Cleav...
Meet Cleaver-X — one binary for:
✂️ Trimming + QC
🧬 FASTA/FASTQ/SAM/BAM
📊 Counting + demux
⚡ Constant-memory streaming
180 MB in 0.17 sec. ~7 MB RAM.
No Python. No C/C++.
Just Rust. 🦀
#Rust #rustsky
Crates
crates.io/crates/Cleav...
And if you use it for the off-label purpose of filtering out reads from not-your-organism, also check out k2tools for faster fastq filtering: github.com/fulcrumgenom...
September 24, 2026 at 8:14 PM
And if you use it for the off-label purpose of filtering out reads from not-your-organism, also check out k2tools for faster fastq filtering: github.com/fulcrumgenom...
SeqFu has a new website!
We tried to make it nicer, but also introduced new in-browser applets.
Try these two:
- 📊 STATS to calculate N50 and plots, for one or more files, or
- 🔍 LESS to have a small preview of FASTQ files with quality, oligo match and more.
telatin.github.io/seqfu2/
We tried to make it nicer, but also introduced new in-browser applets.
Try these two:
- 📊 STATS to calculate N50 and plots, for one or more files, or
- 🔍 LESS to have a small preview of FASTQ files with quality, oligo match and more.
telatin.github.io/seqfu2/
September 24, 2026 at 3:26 PM
SeqFu has a new website!
We tried to make it nicer, but also introduced new in-browser applets.
Try these two:
- 📊 STATS to calculate N50 and plots, for one or more files, or
- 🔍 LESS to have a small preview of FASTQ files with quality, oligo match and more.
telatin.github.io/seqfu2/
We tried to make it nicer, but also introduced new in-browser applets.
Try these two:
- 📊 STATS to calculate N50 and plots, for one or more files, or
- 🔍 LESS to have a small preview of FASTQ files with quality, oligo match and more.
telatin.github.io/seqfu2/
Ever wanted to map sequencing data to a reference genome super easily with a single command?
I have, so I made a tool for it.
PlainMap handles mixed SE/PE, different FASTQ formats, modern + #aDNA, pilot testing, and restartable runs then gives you a BAM + stats.
arxiv.org/abs/2609.183...
I have, so I made a tool for it.
PlainMap handles mixed SE/PE, different FASTQ formats, modern + #aDNA, pilot testing, and restartable runs then gives you a BAM + stats.
arxiv.org/abs/2609.183...
September 23, 2026 at 4:04 PM
Ever wanted to map sequencing data to a reference genome super easily with a single command?
I have, so I made a tool for it.
PlainMap handles mixed SE/PE, different FASTQ formats, modern + #aDNA, pilot testing, and restartable runs then gives you a BAM + stats.
arxiv.org/abs/2609.183...
I have, so I made a tool for it.
PlainMap handles mixed SE/PE, different FASTQ formats, modern + #aDNA, pilot testing, and restartable runs then gives you a BAM + stats.
arxiv.org/abs/2609.183...
I *have* thought about this. I don't yet have a strong security statement. Gravlax does not store sequence. So in that sense, it's not like having the FASTQ/BAM. However, @markgerstein.bsky.social and others have work showing how even e.g. counts/quants can leak data. So I think this is worth study.
September 21, 2026 at 5:38 PM
I *have* thought about this. I don't yet have a strong security statement. Gravlax does not store sequence. So in that sense, it's not like having the FASTQ/BAM. However, @markgerstein.bsky.social and others have work showing how even e.g. counts/quants can leak data. So I think this is worth study.
How small? 11–18 bits per read. That's 9–13× smaller than tag-preserving CRAM and 32–49× smaller than FASTQ.
Small enough to keep an entire cohort online instead of banishing reads to cold storage. But to be useful, the representation should be accurate/faithful.
Small enough to keep an entire cohort online instead of banishing reads to cold storage. But to be useful, the representation should be accurate/faithful.
September 21, 2026 at 3:52 PM
How small? 11–18 bits per read. That's 9–13× smaller than tag-preserving CRAM and 32–49× smaller than FASTQ.
Small enough to keep an entire cohort online instead of banishing reads to cold storage. But to be useful, the representation should be accurate/faithful.
Small enough to keep an entire cohort online instead of banishing reads to cold storage. But to be useful, the representation should be accurate/faithful.
New in expressRNA: native iCLIP analysis. Upload FASTQ — nf-core/clipseq + iCount run as a real Nextflow pipeline: crosslink/peak calling, motif discovery, live genome browser.
expressrna.org
#iCLIP #bioinformatics #clip #expressRNA
expressrna.org
#iCLIP #bioinformatics #clip #expressRNA
September 20, 2026 at 9:26 AM
New in expressRNA: native iCLIP analysis. Upload FASTQ — nf-core/clipseq + iCount run as a real Nextflow pipeline: crosslink/peak calling, motif discovery, live genome browser.
expressrna.org
#iCLIP #bioinformatics #clip #expressRNA
expressrna.org
#iCLIP #bioinformatics #clip #expressRNA
SharkVNTyper 1.2 is out ! another step forward for screening MUC1 kidney disease.
👉 github.com/Nephrogenomi...
#Nephrology #Genomics #RareDisease #ADTKD #MUC1 #Bioinformatics #OpenSource
👉 github.com/Nephrogenomi...
#Nephrology #Genomics #RareDisease #ADTKD #MUC1 #Bioinformatics #OpenSource
GitHub - Nephrogenomics/SharkVNTyper: Systematic screening of the MUC1 27dupC variant (ADTKD-MUC1) from exome FASTQ files: shark read filtering + VNtyper/Kestrel k-mer genotyping, packaged in a docker...
Systematic screening of the MUC1 27dupC variant (ADTKD-MUC1) from exome FASTQ files: shark read filtering + VNtyper/Kestrel k-mer genotyping, packaged in a docker image (Bensouna et al., JASN 2025)...
github.com
September 15, 2026 at 9:50 AM
SharkVNTyper 1.2 is out ! another step forward for screening MUC1 kidney disease.
👉 github.com/Nephrogenomi...
#Nephrology #Genomics #RareDisease #ADTKD #MUC1 #Bioinformatics #OpenSource
👉 github.com/Nephrogenomi...
#Nephrology #Genomics #RareDisease #ADTKD #MUC1 #Bioinformatics #OpenSource
Pipeline release! nf-core/fetchngs v1.13.0 - nf-core/fetchngs v1-13.0 - Palladium Penguin !
Please see the changelog: https://github.com/nf-core/fetchngs/releases/tag/1.13.0
Please see the changelog: https://github.com/nf-core/fetchngs/releases/tag/1.13.0
Release nf-core/fetchngs v1-13.0 - Palladium Penguin · nf-core/fetchngs
What's Changed
New pipeline support
fetchngs now generates samplesheets for ampliseq, mag, metatdenovo, and sarek, alongside the existing atcseq, rnaseq, taxprofiler, and viralrecon support.
fastq-...
github.com
September 15, 2026 at 8:18 AM
Pipeline release! nf-core/fetchngs v1.13.0 - nf-core/fetchngs v1-13.0 - Palladium Penguin !
Please see the changelog: https://github.com/nf-core/fetchngs/releases/tag/1.13.0
Please see the changelog: https://github.com/nf-core/fetchngs/releases/tag/1.13.0
6/
Talk to the wet lab early.
Don’t assume the design is clean.
Ask:
What’s the hypothesis?
Are there replicates?
What are the controls?
Are the conditions randomized?
Good data starts long before you load the fastq.
Talk to the wet lab early.
Don’t assume the design is clean.
Ask:
What’s the hypothesis?
Are there replicates?
What are the controls?
Are the conditions randomized?
Good data starts long before you load the fastq.
September 13, 2026 at 1:15 PM
6/
Talk to the wet lab early.
Don’t assume the design is clean.
Ask:
What’s the hypothesis?
Are there replicates?
What are the controls?
Are the conditions randomized?
Good data starts long before you load the fastq.
Talk to the wet lab early.
Don’t assume the design is clean.
Ask:
What’s the hypothesis?
Are there replicates?
What are the controls?
Are the conditions randomized?
Good data starts long before you load the fastq.
Gravlax is open source (Rust, BSD-3): docs, a Python client, and Colab demos, with v0.2.3 just released.
Stop reprocessing FASTQ every time the annotation moves. Align once, query forever.
github.com/COMBINE-lab/gravlax
Stop reprocessing FASTQ every time the annotation moves. Align once, query forever.
github.com/COMBINE-lab/gravlax
GitHub - COMBINE-lab/gravlax: Annotation-independent molecular-evidence archives for single-cell RNA-seq
Annotation-independent molecular-evidence archives for single-cell RNA-seq - COMBINE-lab/gravlax
github.com
September 12, 2026 at 1:55 PM
Gravlax is open source (Rust, BSD-3): docs, a Python client, and Colab demos, with v0.2.3 just released.
Stop reprocessing FASTQ every time the annotation moves. Align once, query forever.
github.com/COMBINE-lab/gravlax
Stop reprocessing FASTQ every time the annotation moves. Align once, query forever.
github.com/COMBINE-lab/gravlax
How small? A gravlax .aie (annotation independent evidence) archive is 11–18 bits per read: 9–13× smaller than tag-preserving CRAM and 32–49× smaller than FASTQ.
Small enough to keep a whole cohort online instead of banishing reads to cold storage.
Small enough to keep a whole cohort online instead of banishing reads to cold storage.
September 12, 2026 at 1:55 PM
How small? A gravlax .aie (annotation independent evidence) archive is 11–18 bits per read: 9–13× smaller than tag-preserving CRAM and 32–49× smaller than FASTQ.
Small enough to keep a whole cohort online instead of banishing reads to cold storage.
Small enough to keep a whole cohort online instead of banishing reads to cold storage.
4/
But bioinformatics has its pain too.
A bad FASTQ file. Poor replicates. Missing metadata.
You can’t analyze what wasn’t measured right.
But bioinformatics has its pain too.
A bad FASTQ file. Poor replicates. Missing metadata.
You can’t analyze what wasn’t measured right.
September 11, 2026 at 1:15 PM
4/
But bioinformatics has its pain too.
A bad FASTQ file. Poor replicates. Missing metadata.
You can’t analyze what wasn’t measured right.
But bioinformatics has its pain too.
A bad FASTQ file. Poor replicates. Missing metadata.
You can’t analyze what wasn’t measured right.
4/ Level 2: Automating with Bash
Here you start letting the computer work for you.
Instead of:
fastqc sample1.fastq
fastqc sample2.fastq
fastqc sample3.fastq
You write:
for f in *.fastq; do fastqc $f; done
One command. All files.
This is the first taste of freedom.
Here you start letting the computer work for you.
Instead of:
fastqc sample1.fastq
fastqc sample2.fastq
fastqc sample3.fastq
You write:
for f in *.fastq; do fastqc $f; done
One command. All files.
This is the first taste of freedom.
September 10, 2026 at 1:15 PM
4/ Level 2: Automating with Bash
Here you start letting the computer work for you.
Instead of:
fastqc sample1.fastq
fastqc sample2.fastq
fastqc sample3.fastq
You write:
for f in *.fastq; do fastqc $f; done
One command. All files.
This is the first taste of freedom.
Here you start letting the computer work for you.
Instead of:
fastqc sample1.fastq
fastqc sample2.fastq
fastqc sample3.fastq
You write:
for f in *.fastq; do fastqc $f; done
One command. All files.
This is the first taste of freedom.
🧬 **What is your transcriptome telling you?**
From raw FASTQ files to differential expression, pathway enrichment, visualization, and biological interpretation, **Oxford OmicLine** helps researchers turn RNA-Seq datasets into reproducible scientific insights.
📊 **Analyze. Interpret. Discover.**
From raw FASTQ files to differential expression, pathway enrichment, visualization, and biological interpretation, **Oxford OmicLine** helps researchers turn RNA-Seq datasets into reproducible scientific insights.
📊 **Analyze. Interpret. Discover.**
September 5, 2026 at 4:53 PM
🧬 **What is your transcriptome telling you?**
From raw FASTQ files to differential expression, pathway enrichment, visualization, and biological interpretation, **Oxford OmicLine** helps researchers turn RNA-Seq datasets into reproducible scientific insights.
📊 **Analyze. Interpret. Discover.**
From raw FASTQ files to differential expression, pathway enrichment, visualization, and biological interpretation, **Oxford OmicLine** helps researchers turn RNA-Seq datasets into reproducible scientific insights.
📊 **Analyze. Interpret. Discover.**
Something I've been thinking about for a while; with raw FASTQ files at one extreme & count matrices on the other, what's is the "right" archival/transfer format for scRNA-seq data? Big question but big potential "unlocks". Preprint soon (I hope), but here's a sneak peek :): crates.io/crates/gravlax
crates.io: Rust Package Registry
crates.io serves as a central registry for sharing crates, which are packages or libraries written in Rust that you can use to enhance your projects
crates.io
September 3, 2026 at 2:46 PM
Something I've been thinking about for a while; with raw FASTQ files at one extreme & count matrices on the other, what's is the "right" archival/transfer format for scRNA-seq data? Big question but big potential "unlocks". Preprint soon (I hope), but here's a sneak peek :): crates.io/crates/gravlax