7/ But in smaller biotech companies, you might need to handle the entire pipeline—from FASTQ to count matrix and downstream analysis.
November 12, 2025 at 3:15 PM
7/ But in smaller biotech companies, you might need to handle the entire pipeline—from FASTQ to count matrix and downstream analysis.
2/ When you start with raw FASTQ files, there’s a lot happening behind the scenes before you even get to an analysis. Learn the basics.
November 12, 2025 at 3:15 PM
2/ When you start with raw FASTQ files, there’s a lot happening behind the scenes before you even get to an analysis. Learn the basics.
Thank you for your response. FASTQ output is the first step, but I'm also interested to see how many modifications were detected (output in bam format). The problem appeare during sup,5mCG_5hmCG,6mA. I will also try slorado now.
November 10, 2025 at 2:20 PM
Thank you for your response. FASTQ output is the first step, but I'm also interested to see how many modifications were detected (output in bam format). The problem appeare during sup,5mCG_5hmCG,6mA. I will also try slorado now.
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.
November 10, 2025 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.
What are you using Dorado for? If you only need FASTQ output and no modifications, then maybe @hasindu2008.bsky.social and company might have a tool might work. For example BonsonW/slorado: A simplified version of Dorado built on top of S/BLOW5 format. share.google/Kc5sVXTWawcD... might work.
GitHub - BonsonW/slorado: A simplified version of Dorado built on top of S/BLOW5 format.
A simplified version of Dorado built on top of S/BLOW5 format. - BonsonW/slorado
share.google
November 10, 2025 at 1:12 PM
What are you using Dorado for? If you only need FASTQ output and no modifications, then maybe @hasindu2008.bsky.social and company might have a tool might work. For example BonsonW/slorado: A simplified version of Dorado built on top of S/BLOW5 format. share.google/Kc5sVXTWawcD... might work.
Microbiome study of Murrah buffalo mastitis milk with emphasis on Acinetobacter species | BMC Microbiology
https://www.newsbeep.com/il/107694/
Sequence results The raw FastQ sequences upon quality check revealed the dataset comprised 5.5 million to 11.6 million…
https://www.newsbeep.com/il/107694/
Sequence results The raw FastQ sequences upon quality check revealed the dataset comprised 5.5 million to 11.6 million…
Microbiome study of Murrah buffalo mastitis milk with emphasis on Acinetobacter species | BMC Microbiology - Israel News Beep
Sequence results
www.newsbeep.com
October 31, 2025 at 10:45 AM
Microbiome study of Murrah buffalo mastitis milk with emphasis on Acinetobacter species | BMC Microbiology
https://www.newsbeep.com/il/107694/
Sequence results The raw FastQ sequences upon quality check revealed the dataset comprised 5.5 million to 11.6 million…
https://www.newsbeep.com/il/107694/
Sequence results The raw FastQ sequences upon quality check revealed the dataset comprised 5.5 million to 11.6 million…
Microbiome study of Murrah buffalo mastitis milk with emphasis on Acinetobacter species | BMC Microbiology
https://www.europesays.com/ie/155078/
Sequence results The raw FastQ sequences upon quality check revealed the dataset comprised 5.5 million to 11.6 million…
https://www.europesays.com/ie/155078/
Sequence results The raw FastQ sequences upon quality check revealed the dataset comprised 5.5 million to 11.6 million…
Microbiome study of Murrah buffalo mastitis milk with emphasis on Acinetobacter species | BMC Microbiology - Ireland
Sequence results
www.europesays.com
October 31, 2025 at 10:30 AM
Microbiome study of Murrah buffalo mastitis milk with emphasis on Acinetobacter species | BMC Microbiology
https://www.europesays.com/ie/155078/
Sequence results The raw FastQ sequences upon quality check revealed the dataset comprised 5.5 million to 11.6 million…
https://www.europesays.com/ie/155078/
Sequence results The raw FastQ sequences upon quality check revealed the dataset comprised 5.5 million to 11.6 million…
14/
Action items:
Always check how your data were generated.
When in doubt, start from FASTQ and build your own consistent pipeline.
Use GEO or CellxGene metadata—it’s messy, but it’s your map.
Action items:
Always check how your data were generated.
When in doubt, start from FASTQ and build your own consistent pipeline.
Use GEO or CellxGene metadata—it’s messy, but it’s your map.
October 28, 2025 at 1:45 PM
14/
Action items:
Always check how your data were generated.
When in doubt, start from FASTQ and build your own consistent pipeline.
Use GEO or CellxGene metadata—it’s messy, but it’s your map.
Action items:
Always check how your data were generated.
When in doubt, start from FASTQ and build your own consistent pipeline.
Use GEO or CellxGene metadata—it’s messy, but it’s your map.
"The following term was not found in BioProject: PRJEB100828"
☹️
I would have liked to compare timings with FASTQ-DENTAL.
☹️
I would have liked to compare timings with FASTQ-DENTAL.
October 24, 2025 at 12:01 PM
"The following term was not found in BioProject: PRJEB100828"
☹️
I would have liked to compare timings with FASTQ-DENTAL.
☹️
I would have liked to compare timings with FASTQ-DENTAL.
🧬 From FASTQ files → reproducible pipelines → biological insights! Mariam Sulaiman from IITA Nigeria shares her first experience with @nextflow.io and @nf-co.re, detecting Kappa variants using nf-core/viralrecon workflow
October 23, 2025 at 2:55 PM
🧬 From FASTQ files → reproducible pipelines → biological insights! Mariam Sulaiman from IITA Nigeria shares her first experience with @nextflow.io and @nf-co.re, detecting Kappa variants using nf-core/viralrecon workflow
RESULTS!!!
Okay so got 12k reads (bug seems very hard to crack) but the kind folks at @plasmidsaurus.bsky.social offered to rerun. In the meantime, I'm getting some very strong blast hits for a recently discovered species, Edaphobacter flagellatus.
FASTQ DATA:
drive.google.com/drive/folder...
Okay so got 12k reads (bug seems very hard to crack) but the kind folks at @plasmidsaurus.bsky.social offered to rerun. In the meantime, I'm getting some very strong blast hits for a recently discovered species, Edaphobacter flagellatus.
FASTQ DATA:
drive.google.com/drive/folder...
October 22, 2025 at 1:15 AM
RESULTS!!!
Okay so got 12k reads (bug seems very hard to crack) but the kind folks at @plasmidsaurus.bsky.social offered to rerun. In the meantime, I'm getting some very strong blast hits for a recently discovered species, Edaphobacter flagellatus.
FASTQ DATA:
drive.google.com/drive/folder...
Okay so got 12k reads (bug seems very hard to crack) but the kind folks at @plasmidsaurus.bsky.social offered to rerun. In the meantime, I'm getting some very strong blast hits for a recently discovered species, Edaphobacter flagellatus.
FASTQ DATA:
drive.google.com/drive/folder...
This was the result of a discussion where someone asked if there was a tool out there that can show the first X bases of a fastq file. Seqkit was the first out the gate which you can see here: github.com/shenwei356/s...
a function equivalent to head but for FASTX bases rather than lines/bytes (head) or records (seqkit head)? · Issue #548 · shenwei356/seqkit
from @bede Does anyone know of an existing—preferably packaged—equivalent to head but for FASTX bases rather than lines/bytes (head) or records (seqkit head)? I mean the base aware equivalent of un...
github.com
October 21, 2025 at 12:15 AM
This was the result of a discussion where someone asked if there was a tool out there that can show the first X bases of a fastq file. Seqkit was the first out the gate which you can see here: github.com/shenwei356/s...
🚀 New in Fasten: fasten_head
Unix head, but FASTQ-aware 🧬
✅ Get first N reads (not just lines!)
✅ Works with paired-end reads
✅ Can limit by bases OR reads
✅ Blazingly fast (it's Rust 🦀)
cat huge.fq | fasten_head -r 1000
Stop doing math with -n. Let the tool understand your data.
Unix head, but FASTQ-aware 🧬
✅ Get first N reads (not just lines!)
✅ Works with paired-end reads
✅ Can limit by bases OR reads
✅ Blazingly fast (it's Rust 🦀)
cat huge.fq | fasten_head -r 1000
Stop doing math with -n. Let the tool understand your data.
October 21, 2025 at 12:13 AM
🚀 New in Fasten: fasten_head
Unix head, but FASTQ-aware 🧬
✅ Get first N reads (not just lines!)
✅ Works with paired-end reads
✅ Can limit by bases OR reads
✅ Blazingly fast (it's Rust 🦀)
cat huge.fq | fasten_head -r 1000
Stop doing math with -n. Let the tool understand your data.
Unix head, but FASTQ-aware 🧬
✅ Get first N reads (not just lines!)
✅ Works with paired-end reads
✅ Can limit by bases OR reads
✅ Blazingly fast (it's Rust 🦀)
cat huge.fq | fasten_head -r 1000
Stop doing math with -n. Let the tool understand your data.
But in reality, each sample might have multiple fastq files, like:
simpleaf quant --reads1 L1_R1.fq,L2_R1.fq,L3_R1.fq \
--reads2 L1_R2.fq,L2_R2.fq,L3_R2.fq
simpleaf quant --reads1 L1_R1.fq,L2_R1.fq,L3_R1.fq \
--reads2 L1_R2.fq,L2_R2.fq,L3_R2.fq
October 19, 2025 at 1:45 PM
But in reality, each sample might have multiple fastq files, like:
simpleaf quant --reads1 L1_R1.fq,L2_R1.fq,L3_R1.fq \
--reads2 L1_R2.fq,L2_R2.fq,L3_R2.fq
simpleaf quant --reads1 L1_R1.fq,L2_R1.fq,L3_R1.fq \
--reads2 L1_R2.fq,L2_R2.fq,L3_R2.fq
メタゲノムを対象に検索してみたが、かなり類似度の低い配列も取ってこれるようだ。BLASTNの代わりになるか？代わりになるのだとしたら、あと1年早く出して欲しかったな…。いやGitHubには前からあったみたいなので、気付かなかった俺が悪いのか。BLAST DBに対応していれば助かるんだが、FASTA/FASTQしか対応していないようだ。NCBI ntのFASTAを用意しないといけないのか…。めんどくせーなー。
October 18, 2025 at 5:38 PM
メタゲノムを対象に検索してみたが、かなり類似度の低い配列も取ってこれるようだ。BLASTNの代わりになるか？代わりになるのだとしたら、あと1年早く出して欲しかったな…。いやGitHubには前からあったみたいなので、気付かなかった俺が悪いのか。BLAST DBに対応していれば助かるんだが、FASTA/FASTQしか対応していないようだ。NCBI ntのFASTAを用意しないといけないのか…。めんどくせーなー。
#ERGAReads | The #VGP @genomeark team built rdeval, a tool to quickly compute, store & visualise sequencing read stats. From FASTQ to snapshot files & visual reports, speeding up data quality checks at scale.
🔗 academic.oup.com/bioinformati... @giulio_formenti @erichjarvis
🔗 academic.oup.com/bioinformati... @giulio_formenti @erichjarvis
October 15, 2025 at 1:30 PM
#ERGAReads | The #VGP @genomeark team built rdeval, a tool to quickly compute, store & visualise sequencing read stats. From FASTQ to snapshot files & visual reports, speeding up data quality checks at scale.
🔗 academic.oup.com/bioinformati... @giulio_formenti @erichjarvis
🔗 academic.oup.com/bioinformati... @giulio_formenti @erichjarvis
It takes in (paired) fastq/a files, a JSON expected read structure, an optional expected combinations TSV and a strategy for extracting and matching variable regions and outputs count tables against your library.
October 13, 2025 at 2:36 PM
It takes in (paired) fastq/a files, a JSON expected read structure, an optional expected combinations TSV and a strategy for extracting and matching variable regions and outputs count tables against your library.
How do you deal with different library prep effects? We have done something very similar using BUSCO genes and see >50% variation in genome size for the same inbred line depending on what fastq dataset we download from the SRA. My guess is library prep (especially PCR reps) affects repeat content.
October 11, 2025 at 7:04 PM
How do you deal with different library prep effects? We have done something very similar using BUSCO genes and see >50% variation in genome size for the same inbred line depending on what fastq dataset we download from the SRA. My guess is library prep (especially PCR reps) affects repeat content.
Do you want to link genomic variants to functional gene expression - cell by cell?
SDR-seq makes it possible; an experimental method connecting coding and non-coding variants to expression in single cells.
Proud to have contributed a custom FASTQ-processing tool to this great collaborative project.
SDR-seq makes it possible; an experimental method connecting coding and non-coding variants to expression in single cells.
Proud to have contributed a custom FASTQ-processing tool to this great collaborative project.
EMBL scientists have created a more sensitive single-cell sequencing tool for genomic variants and RNA in the same single cell.
Known as SDR-seq, the tool has unprecedented scale, precision, and speed to characterise variants and link them to functions and disease.
www.embl.org/news/science...
Known as SDR-seq, the tool has unprecedented scale, precision, and speed to characterise variants and link them to functions and disease.
www.embl.org/news/science...
New tool offers single-cell study of specific genetic variants | EMBL
Scientists developed a more sensitive single-cell sequencing tool linking genomic variants & RNA in the same cell uncover links to disease.
www.embl.org
October 10, 2025 at 2:42 PM
Do you want to link genomic variants to functional gene expression - cell by cell?
SDR-seq makes it possible; an experimental method connecting coding and non-coding variants to expression in single cells.
Proud to have contributed a custom FASTQ-processing tool to this great collaborative project.
SDR-seq makes it possible; an experimental method connecting coding and non-coding variants to expression in single cells.
Proud to have contributed a custom FASTQ-processing tool to this great collaborative project.
Trying to figure out how long it will take these fastq files to transfer. 140 files with about 9 million reads each. Any guesses?
October 8, 2025 at 7:13 PM
Trying to figure out how long it will take these fastq files to transfer. 140 files with about 9 million reads each. Any guesses?
🎓 Mariam Sulaiman from IITA- From FASTQ to Kappa: My First Experience with @nf-co.re /viralrecon
summit.nextflow.io/2025/virtual...
summit.nextflow.io/2025/virtual...
From FASTQ to Kappa: My First Experience with nf-core/viralrecon | Mariam Sulaiman undefined | Nextflow Summit 2025
Join us at the Nextflow Summit 2025 for the latest developments and innovations from the Nextflow world.
summit.nextflow.io
October 8, 2025 at 8:32 AM
🎓 Mariam Sulaiman from IITA- From FASTQ to Kappa: My First Experience with @nf-co.re /viralrecon
summit.nextflow.io/2025/virtual...
summit.nextflow.io/2025/virtual...
A significant OpenZL theme is genomic data compression. Users are eager for benchmarks against CRAM, FASTA, FASTQ, SAM, and VCF. It shows promise for tackling large datasets, especially challenging nanopore data. #Genomics 2/5
October 7, 2025 at 7:00 PM
A significant OpenZL theme is genomic data compression. Users are eager for benchmarks against CRAM, FASTA, FASTQ, SAM, and VCF. It shows promise for tackling large datasets, especially challenging nanopore data. #Genomics 2/5
🚀 The Dovetail Analysis Portal (DAP) just expanded to support epigenetics!
Go from FASTQ files to interactive 3D genomic insights — fast, simple, and affordable.
👉 Sign up to try the test dataset or book a run-through:
🔗 portal.cantatabio.co...
🔗 cantatabio.com/dovet...
Go from FASTQ files to interactive 3D genomic insights — fast, simple, and affordable.
👉 Sign up to try the test dataset or book a run-through:
🔗 portal.cantatabio.co...
🔗 cantatabio.com/dovet...
October 7, 2025 at 7:27 AM
🚀 The Dovetail Analysis Portal (DAP) just expanded to support epigenetics!
Go from FASTQ files to interactive 3D genomic insights — fast, simple, and affordable.
👉 Sign up to try the test dataset or book a run-through:
🔗 portal.cantatabio.co...
🔗 cantatabio.com/dovet...
Go from FASTQ files to interactive 3D genomic insights — fast, simple, and affordable.
👉 Sign up to try the test dataset or book a run-through:
🔗 portal.cantatabio.co...
🔗 cantatabio.com/dovet...
There is one thing that surprises me in ONT - their attempt to combine data acquisition with real-time data analysis. IMO, just data acqusition followed by a separate analysis is a better approach.
Although POD5 requires more space than FASTQ, high capacity HDDs are cheaper than graphic cards.
Although POD5 requires more space than FASTQ, high capacity HDDs are cheaper than graphic cards.
October 2, 2025 at 5:37 PM
There is one thing that surprises me in ONT - their attempt to combine data acquisition with real-time data analysis. IMO, just data acqusition followed by a separate analysis is a better approach.
Although POD5 requires more space than FASTQ, high capacity HDDs are cheaper than graphic cards.
Although POD5 requires more space than FASTQ, high capacity HDDs are cheaper than graphic cards.
And today's (useless) figure is that the mean depth observed in a bam file is linearly associated with the number of reads in the corresponding fastq files.
September 29, 2025 at 5:04 PM
And today's (useless) figure is that the mean depth observed in a bam file is linearly associated with the number of reads in the corresponding fastq files.