🧬💾 𝙂𝙚𝙣𝙤𝙢𝙞𝙘 𝘿𝙖𝙩𝙖 𝘾𝙤𝙢𝙥𝙧𝙚𝙨𝙨𝙞𝙤𝙣 𝙖𝙣𝙙 𝙋𝙧𝙤𝙘𝙚𝙨𝙨𝙞𝙣𝙜 covers #FASTA, #FASTQ, SAM/BAM, VCF & single-cell compression, alongside MPEG-G standards, GA4GH & #neuralgenomiccompression.
🔗 www.worldscientific.com/worldscibooks/10.1142/14895
🎯 WSTWTR30 for 30% OFF
🔗 www.worldscientific.com/worldscibooks/10.1142/14895
🎯 WSTWTR30 for 30% OFF
November 11, 2026 at 12:52 AM
🧬💾 𝙂𝙚𝙣𝙤𝙢𝙞𝙘 𝘿𝙖𝙩𝙖 𝘾𝙤𝙢𝙥𝙧𝙚𝙨𝙨𝙞𝙤𝙣 𝙖𝙣𝙙 𝙋𝙧𝙤𝙘𝙚𝙨𝙨𝙞𝙣𝙜 covers #FASTA, #FASTQ, SAM/BAM, VCF & single-cell compression, alongside MPEG-G standards, GA4GH & #neuralgenomiccompression.
🔗 www.worldscientific.com/worldscibooks/10.1142/14895
🎯 WSTWTR30 for 30% OFF
🔗 www.worldscientific.com/worldscibooks/10.1142/14895
🎯 WSTWTR30 for 30% OFF
Introducing ONT-LibQC 🧬
QC your CUT&RUN, CUT&Tag or Micro-C libraries with nanopore sequencing before committing to costly Illumina. Results overnight, ~$10 per library when pooling 3.
Open source, free web server, most model organisms, and no coding needed.
ontlibqc.org
We’d love your feedback!
QC your CUT&RUN, CUT&Tag or Micro-C libraries with nanopore sequencing before committing to costly Illumina. Results overnight, ~$10 per library when pooling 3.
Open source, free web server, most model organisms, and no coding needed.
ontlibqc.org
We’d love your feedback!
November 6, 2026 at 3:42 PM
Introducing ONT-LibQC 🧬
QC your CUT&RUN, CUT&Tag or Micro-C libraries with nanopore sequencing before committing to costly Illumina. Results overnight, ~$10 per library when pooling 3.
Open source, free web server, most model organisms, and no coding needed.
ontlibqc.org
We’d love your feedback!
QC your CUT&RUN, CUT&Tag or Micro-C libraries with nanopore sequencing before committing to costly Illumina. Results overnight, ~$10 per library when pooling 3.
Open source, free web server, most model organisms, and no coding needed.
ontlibqc.org
We’d love your feedback!
Why do I think it's more robust? Well, I've been dog-fooding it extensively this last month. I've used it to convert ~10,000 10-90X whole genomes to fastq, as well as do ranged conversions of many more archives to peek at what's inside.
November 9, 2026 at 6:07 PM
Why do I think it's more robust? Well, I've been dog-fooding it extensively this last month. I've used it to convert ~10,000 10-90X whole genomes to fastq, as well as do ranged conversions of many more archives to peek at what's inside.
With methylation calling does it output a BAM with tags or those tags on the FASTQ?
November 5, 2026 at 1:06 PM
With methylation calling does it output a BAM with tags or those tags on the FASTQ?
🧬 New to RNA-seq analysis? Join our online course (15–19 March 2027)! Learn the complete workflow, from raw FASTQ files to differential expression, visualisation & pathway analysis. No command-line experience needed!
www.physalia-courses.org/courses-work...
#RNAseq
www.physalia-courses.org/courses-work...
#RNAseq
RNAseq data analysis for Beginners
15-19 March 2027
www.physalia-courses.org
November 6, 2026 at 9:14 AM
🧬 New to RNA-seq analysis? Join our online course (15–19 March 2027)! Learn the complete workflow, from raw FASTQ files to differential expression, visualisation & pathway analysis. No command-line experience needed!
www.physalia-courses.org/courses-work...
#RNAseq
www.physalia-courses.org/courses-work...
#RNAseq
5/ Example: AI writes you an awk command to parse FASTQ.
It runs fast. But it trims the wrong bases.
Without knowing awk, you trust junk data.
It runs fast. But it trims the wrong bases.
Without knowing awk, you trust junk data.
November 4, 2026 at 2:45 PM
5/ Example: AI writes you an awk command to parse FASTQ.
It runs fast. But it trims the wrong bases.
Without knowing awk, you trust junk data.
It runs fast. But it trims the wrong bases.
Without knowing awk, you trust junk data.
New preprint on Zenodo: dānaSeq nanopore_live: real-time processing of Oxford Nanopore metagenomic reads
doi.org/10.5281/zenodo.23899192
doi.org/10.5281/zenodo.23899192
dānaSeq nanopore_live: real-time processing of Oxford Nanopore metagenomic reads
Motivation: During an Oxford Nanopore run, MinKNOW writes basecalled reads to disk as a growing series of small FASTQ files. On ships and at field stations, analysis must run on the sequencing workstation, keep up with the run, and end with a loss-free move of the data to…
doi.org
November 5, 2026 at 4:46 PM
New preprint on Zenodo: dānaSeq nanopore_live: real-time processing of Oxford Nanopore metagenomic reads
doi.org/10.5281/zenodo.23899192
doi.org/10.5281/zenodo.23899192
At opening of #iBOL2026 in Bangkok. First impression is the prominence of companies such as @biokeaai.bsky.social and spcfy.io, together with @pensoft.net.
spcfy | DNA Metabarcoding Infrastructure for Labs, Bioinformaticians & Data Users
spcfy turns raw FASTQ data into reproducible, comparable biodiversity data. Standardized pipelines for sequencing labs, bioinformaticians and data users, with full data ownership and EU hosting
spcfy.io
November 3, 2026 at 2:10 AM
At opening of #iBOL2026 in Bangkok. First impression is the prominence of companies such as @biokeaai.bsky.social and spcfy.io, together with @pensoft.net.
would you consider integrating it into polars-bio project: biodatageeks.org/polars-bio/
They have fasta/fastq readers, but I bet yours is better.
While it's cool to have bindings to other languages, as already requested, I'm personally more interested in bindings to ecosystems, if I may😁
They have fasta/fastq readers, but I bet yours is better.
While it's cool to have bindings to other languages, as already requested, I'm personally more interested in bindings to ecosystems, if I may😁
polars-bio
biodatageeks.org
November 2, 2026 at 10:26 AM
would you consider integrating it into polars-bio project: biodatageeks.org/polars-bio/
They have fasta/fastq readers, but I bet yours is better.
While it's cool to have bindings to other languages, as already requested, I'm personally more interested in bindings to ecosystems, if I may😁
They have fasta/fastq readers, but I bet yours is better.
While it's cool to have bindings to other languages, as already requested, I'm personally more interested in bindings to ecosystems, if I may😁
Learn RNA-seq: From FASTQ to Counts at your own pace!
#Research #Instats
Full details and registration in the first reply.
#Research #Instats
Full details and registration in the first reply.
October 31, 2026 at 1:40 PM
Learn RNA-seq: From FASTQ to Counts at your own pace!
#Research #Instats
Full details and registration in the first reply.
#Research #Instats
Full details and registration in the first reply.
Available on demand, at your own pace.
Full details and registration: https://instats.org/seminar/rna-seq-from-fastq-to-counts-1?utm_source=bluesky
Full details and registration: https://instats.org/seminar/rna-seq-from-fastq-to-counts-1?utm_source=bluesky
October 31, 2026 at 1:40 PM
Available on demand, at your own pace.
Full details and registration: https://instats.org/seminar/rna-seq-from-fastq-to-counts-1?utm_source=bluesky
Full details and registration: https://instats.org/seminar/rna-seq-from-fastq-to-counts-1?utm_source=bluesky
previous post: chatomics! How to preprocess GEO bulk RNAseq data with salmon divingintogeneticsandgenomics.com/post/how-to...
How to preprocess GEO bulk RNAseq data with salmon | Chatomics
Install fastq-dl To easily download fastq from GEO or ENA, use fastq-dl
Assume you already have conda installed, do the following:
conda config --add channels conda-forge conda config --add channels bioconda conda create -n fastq_download -c conda-forge -c bioconda fastq-dl conda activate fastq_download Tip: use mamba if conda is too slow for you. They are all big snakes!!
We will use bulk RNAseq data from this GEO accession ID: https://www.
divingintogeneticsandgenomics.com
October 28, 2026 at 1:45 PM
previous post: chatomics! How to preprocess GEO bulk RNAseq data with salmon divingintogeneticsandgenomics.com/post/how-to...
3/6
The method uses 2,145 phylogeny-derived markers identified from 26,813 genomes.
It works directly with genome assemblies (FASTA) or raw sequencing reads (FASTQ), without requiring conventional read mapping.
The method uses 2,145 phylogeny-derived markers identified from 26,813 genomes.
It works directly with genome assemblies (FASTA) or raw sequencing reads (FASTQ), without requiring conventional read mapping.
October 28, 2026 at 1:44 PM
3/6
The method uses 2,145 phylogeny-derived markers identified from 26,813 genomes.
It works directly with genome assemblies (FASTA) or raw sequencing reads (FASTQ), without requiring conventional read mapping.
The method uses 2,145 phylogeny-derived markers identified from 26,813 genomes.
It works directly with genome assemblies (FASTA) or raw sequencing reads (FASTQ), without requiring conventional read mapping.
2/
Bioinformatics runs on plain text:
FASTA. FASTQ. SAM. BED. GTF.
They look messy.
Unix commands clean them like magic.
Bioinformatics runs on plain text:
FASTA. FASTQ. SAM. BED. GTF.
They look messy.
Unix commands clean them like magic.
October 25, 2026 at 2:15 PM
2/
Bioinformatics runs on plain text:
FASTA. FASTQ. SAM. BED. GTF.
They look messy.
Unix commands clean them like magic.
Bioinformatics runs on plain text:
FASTA. FASTQ. SAM. BED. GTF.
They look messy.
Unix commands clean them like magic.
🧬 Right command, wrong file = 𝘀𝗶𝗹𝗲𝗻𝘁 𝗲𝗿𝗿𝗼𝗿𝘀.
A FASTQ record has 𝟰 𝗹𝗶𝗻𝗲𝘀. Check yours before analysis:
zcat reads.fastq.gz | awk 'END{print NR%4}'
The result must be 𝟬. Guide to FASTA, FASTQ, BAM and VCF 👇
theomicshub.com/tutorials/bi...
#Bioinformatics #NGS
A FASTQ record has 𝟰 𝗹𝗶𝗻𝗲𝘀. Check yours before analysis:
zcat reads.fastq.gz | awk 'END{print NR%4}'
The result must be 𝟬. Guide to FASTA, FASTQ, BAM and VCF 👇
theomicshub.com/tutorials/bi...
#Bioinformatics #NGS
Biological Data Formats | The Omics Hub
Read FASTA, FASTQ, SAM/BAM, VCF, GTF/GFF, and count matrices with confidence before running analysis pipelines.
theomicshub.com
October 19, 2026 at 6:11 AM
🧬 Right command, wrong file = 𝘀𝗶𝗹𝗲𝗻𝘁 𝗲𝗿𝗿𝗼𝗿𝘀.
A FASTQ record has 𝟰 𝗹𝗶𝗻𝗲𝘀. Check yours before analysis:
zcat reads.fastq.gz | awk 'END{print NR%4}'
The result must be 𝟬. Guide to FASTA, FASTQ, BAM and VCF 👇
theomicshub.com/tutorials/bi...
#Bioinformatics #NGS
A FASTQ record has 𝟰 𝗹𝗶𝗻𝗲𝘀. Check yours before analysis:
zcat reads.fastq.gz | awk 'END{print NR%4}'
The result must be 𝟬. Guide to FASTA, FASTQ, BAM and VCF 👇
theomicshub.com/tutorials/bi...
#Bioinformatics #NGS
2/ Setup: BCL to FASTQ with bcl2fastq, then a SHARE-seq pipeline. The first QC run died at the naming check:
“No fastq with matched naming format detected”
The pipeline wants S1_R1_001.fastq.gz. bcl2fastq wrote Undetermined_S0.
“No fastq with matched naming format detected”
The pipeline wants S1_R1_001.fastq.gz. bcl2fastq wrote Undetermined_S0.
October 16, 2026 at 1:45 PM
2/ Setup: BCL to FASTQ with bcl2fastq, then a SHARE-seq pipeline. The first QC run died at the naming check:
“No fastq with matched naming format detected”
The pipeline wants S1_R1_001.fastq.gz. bcl2fastq wrote Undetermined_S0.
“No fastq with matched naming format detected”
The pipeline wants S1_R1_001.fastq.gz. bcl2fastq wrote Undetermined_S0.
1/ I’ve run bcl2fastq before. I know what a symlink is.
Basic stuff. It still shaped how a 1.2 TB SHARE-seq run went last week, when Claude Code proposed renaming every FASTQ with symlinks and I hit reject to ask why.
Basic stuff. It still shaped how a 1.2 TB SHARE-seq run went last week, when Claude Code proposed renaming every FASTQ with symlinks and I hit reject to ask why.
October 16, 2026 at 1:45 PM
1/ I’ve run bcl2fastq before. I know what a symlink is.
Basic stuff. It still shaped how a 1.2 TB SHARE-seq run went last week, when Claude Code proposed renaming every FASTQ with symlinks and I hit reject to ask why.
Basic stuff. It still shaped how a 1.2 TB SHARE-seq run went last week, when Claude Code proposed renaming every FASTQ with symlinks and I hit reject to ask why.
Oh sweet, new autocycler version dropped. General performance improvement and unaligned BAM support for processing basecalled output directly (though I feel like regular users would still want a filtered fastq for their assemblies).
github.com/rrwick/Autoc...
github.com/rrwick/Autoc...
Release Autocycler v0.8.0 · rrwick/Autocycler
This release:
Adds support for unaligned BAM (uBAM) input reads in addition to FASTQ format. uBAM is the default format for basecalled ONT reads.
Has miscellaneous code refactoring and optimisatio...
github.com
October 11, 2026 at 1:20 PM
Oh sweet, new autocycler version dropped. General performance improvement and unaligned BAM support for processing basecalled output directly (though I feel like regular users would still want a filtered fastq for their assemblies).
github.com/rrwick/Autoc...
github.com/rrwick/Autoc...
Both pac bio and ont have made uBAM a first class output, and while I was kinda against it at first, I can see the advantages, especially when taking methylation into account. You can always get fastq out of bam anyway.
October 12, 2026 at 12:28 AM
Both pac bio and ont have made uBAM a first class output, and while I was kinda against it at first, I can see the advantages, especially when taking methylation into account. You can always get fastq out of bam anyway.
How much sequencing data do you actually need for SARS-CoV-2 genomic surveillance?
Yered Ortega was a summer intern last year who set out to test whether downsampling FASTQ files can slash compute time without sacrificing consensus quality or lineage calls.
Preprint: doi.org/10.64898/202...
Yered Ortega was a summer intern last year who set out to test whether downsampling FASTQ files can slash compute time without sacrificing consensus quality or lineage calls.
Preprint: doi.org/10.64898/202...
doi.org
October 9, 2026 at 4:30 PM
How much sequencing data do you actually need for SARS-CoV-2 genomic surveillance?
Yered Ortega was a summer intern last year who set out to test whether downsampling FASTQ files can slash compute time without sacrificing consensus quality or lineage calls.
Preprint: doi.org/10.64898/202...
Yered Ortega was a summer intern last year who set out to test whether downsampling FASTQ files can slash compute time without sacrificing consensus quality or lineage calls.
Preprint: doi.org/10.64898/202...
Trimming down massive FASTQ files dropped total pipeline runtime from ~1,400 seconds to under 200 seconds with SeqKit and ~400 seconds with BBNorm.
Kudos to Yered Ortega for leading this work at Utah Public Health Laboratory!
Kudos to Yered Ortega for leading this work at Utah Public Health Laboratory!
October 9, 2026 at 4:30 PM
Trimming down massive FASTQ files dropped total pipeline runtime from ~1,400 seconds to under 200 seconds with SeqKit and ~400 seconds with BBNorm.
Kudos to Yered Ortega for leading this work at Utah Public Health Laboratory!
Kudos to Yered Ortega for leading this work at Utah Public Health Laboratory!
Authors published a paper in Biorxiv, they used FASTA in the study. Including #RRIDs will make this less ambiguous.
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #STMpublishing #OpenScience
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #STMpublishing #OpenScience
Byte-exact, format-aware compression for FASTA, FASTQ, BED and VCF files
www.biorxiv.org
October 8, 2026 at 12:00 PM
Authors published a paper in Biorxiv, they used FASTA in the study. Including #RRIDs will make this less ambiguous.
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #STMpublishing #OpenScience
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #STMpublishing #OpenScience
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