just another day of working on a Node.js project. today it is fastq.
August 8, 2025 at 6:00 PM
just another day of working on a Node.js project. today it is fastq.
Efficient sampling of reads (with replacement). www.biorxiv.org/content/10.6...
fastQpick: scalable bootstrap and subsampling of FASTQ reads
fastQpick is a command-line tool and Python library for sampling FASTQ reads with replacement. Sampling with replacement turns a single FASTQ file into an arbitrary number of bootstrap replicates, whi...
www.biorxiv.org
June 26, 2026 at 6:05 AM
Efficient sampling of reads (with replacement). www.biorxiv.org/content/10.6...
Ok; mim (github.com/COMBINE-lab/...) preprint submitted! Excited for folks to see it and share thoughts. The key takeaway; mim allows the quick, one-time, building of a small auxiliary index that then allows scaling gzipped FASTQ parsing linearly in # of threads. 1/2
GitHub - COMBINE-lab/mim: A small, auxiliary index to massively improve parallel fastq parsing
A small, auxiliary index to massively improve parallel fastq parsing - COMBINE-lab/mim
github.com
November 25, 2025 at 2:13 PM
Ok; mim (github.com/COMBINE-lab/...) preprint submitted! Excited for folks to see it and share thoughts. The key takeaway; mim allows the quick, one-time, building of a small auxiliary index that then allows scaling gzipped FASTQ parsing linearly in # of threads. 1/2
@wytamma.bsky.social : so, it took a little bit of extra time (not the flight back from the CZI meeting), but I decided to just f#&$ing do it, and the basic code to build and parse with the auxiliary fastq index is working (github.com/COMBINE-lab/...). 1/2
GitHub - COMBINE-lab/mim: A small, auxiliary index to massively improve parallel fastq parsing
A small, auxiliary index to massively improve parallel fastq parsing - COMBINE-lab/mim
github.com
November 19, 2025 at 3:01 AM
@wytamma.bsky.social : so, it took a little bit of extra time (not the flight back from the CZI meeting), but I decided to just f#&$ing do it, and the basic code to build and parse with the auxiliary fastq index is working (github.com/COMBINE-lab/...). 1/2
Giving me an uncompressed fastq file should count as bullying
February 2, 2026 at 5:28 PM
Giving me an uncompressed fastq file should count as bullying
I made a little swiss army knife tool for quickly inspecting FASTA/FASTQ sequences, including GC content, codon analysis, reverse complement, and file format conversions: 🖥️ 🧬
42basepairs.com/tools/sequen...
42basepairs.com/tools/sequen...
Sequence Analysis - 42basepairs
Bioinformatics sequence analysis on FASTA and FASTQ files, including reverse complement, GC content calculations, codon usage analysis, and converting your files to FASTA, FASTQ, or SAM format
42basepairs.com
November 27, 2024 at 7:35 PM
I made a little swiss army knife tool for quickly inspecting FASTA/FASTQ sequences, including GC content, codon analysis, reverse complement, and file format conversions: 🖥️ 🧬
42basepairs.com/tools/sequen...
42basepairs.com/tools/sequen...
Woot! The mim preprint is live now. www.biorxiv.org/content/10.1...
Happy Thanksgiving!
Cc @curiouscoding.nl
Happy Thanksgiving!
Cc @curiouscoding.nl
mim: A lightweight auxiliary index to enable fast, parallel, gzipped FASTQ parsing
The FASTQ file format is the lingua franca of primary data distribution and processing across most of bioinformatics. Over time, the compression, storage, transmission, and decompression of gzip compr...
www.biorxiv.org
November 27, 2025 at 5:22 PM
Woot! The mim preprint is live now. www.biorxiv.org/content/10.1...
Happy Thanksgiving!
Cc @curiouscoding.nl
Happy Thanksgiving!
Cc @curiouscoding.nl
New preprint! Deacon is a versatile tool for filtering FASTA/FASTQ files and streams at hundreds of megabases per second using minimizers, built with rapid metagenomic host depletion in mind, but equally useful for search.
github.com/bede/deacon
github.com/bede/deacon
Deacon: fast sequence filtering and contaminant depletion https://www.biorxiv.org/content/10.1101/2025.06.09.658732v1
June 13, 2025 at 1:25 PM
New preprint! Deacon is a versatile tool for filtering FASTA/FASTQ files and streams at hundreds of megabases per second using minimizers, built with rapid metagenomic host depletion in mind, but equally useful for search.
github.com/bede/deacon
github.com/bede/deacon
Dehosting compressed FASTQ at 150Mbp/s on a MacBook
github.com/bede/deacon
github.com/bede/deacon
May 9, 2025 at 2:23 PM
Dehosting compressed FASTQ at 150Mbp/s on a MacBook
github.com/bede/deacon
github.com/bede/deacon
If you need to sample reads (with or without replacement) from FASTQ files you may find the fastQpick utility by Joseph Rich super useful: github.com/pachterlab/f...
GitHub - pachterlab/fastQpick
Contribute to pachterlab/fastQpick development by creating an account on GitHub.
github.com
January 27, 2025 at 1:11 AM
If you need to sample reads (with or without replacement) from FASTQ files you may find the fastQpick utility by Joseph Rich super useful: github.com/pachterlab/f...
New blog post!
Ever seen a genome assembly in FASTQ format instead of FASTA? Dorado polish from @nanoporetech.com can do it, and I took a closer look:
rrwick.github.io/2025/02/19/f...
Ever seen a genome assembly in FASTQ format instead of FASTA? Dorado polish from @nanoporetech.com can do it, and I took a closer look:
rrwick.github.io/2025/02/19/f...
FASTQ assemblies with Dorado polish
a blog for miscellaneous bioinformatics stuff
rrwick.github.io
February 19, 2025 at 5:54 AM
New blog post!
Ever seen a genome assembly in FASTQ format instead of FASTA? Dorado polish from @nanoporetech.com can do it, and I took a closer look:
rrwick.github.io/2025/02/19/f...
Ever seen a genome assembly in FASTQ format instead of FASTA? Dorado polish from @nanoporetech.com can do it, and I took a closer look:
rrwick.github.io/2025/02/19/f...
fqgrep release 1.1.0 now speeds up searching FASTQ files!
Thank-you to both Markus Schlegel from @activegroupgmbh.bsky.social for updating seq_io and Nicholas D. Crosbie of grepq for some competition and inspiration.
See more: github.com/fulcrumgenom...
Thank-you to both Markus Schlegel from @activegroupgmbh.bsky.social for updating seq_io and Nicholas D. Crosbie of grepq for some competition and inspiration.
See more: github.com/fulcrumgenom...
GitHub - fulcrumgenomics/fqgrep: Grep for FASTQ files
Grep for FASTQ files. Contribute to fulcrumgenomics/fqgrep development by creating an account on GitHub.
github.com
March 14, 2025 at 5:45 PM
fqgrep release 1.1.0 now speeds up searching FASTQ files!
Thank-you to both Markus Schlegel from @activegroupgmbh.bsky.social for updating seq_io and Nicholas D. Crosbie of grepq for some competition and inspiration.
See more: github.com/fulcrumgenom...
Thank-you to both Markus Schlegel from @activegroupgmbh.bsky.social for updating seq_io and Nicholas D. Crosbie of grepq for some competition and inspiration.
See more: github.com/fulcrumgenom...
But `>` is a valid quality score in FASTQ.
June 24, 2025 at 5:00 PM
But `>` is a valid quality score in FASTQ.
ish is a grep-like CLI tool that uses optimal alignment instead of exact matching.
It’s record-type aware, supporting line, FASTA, and FASTQ records.
Built in Mojo as a proof of concept for bioinformatics.
🧵1/5
It’s record-type aware, supporting line, FASTA, and FASTQ records.
Built in Mojo as a proof of concept for bioinformatics.
🧵1/5
Ish: SIMD and GPU Accelerated Local and Semi-Global Alignment as a CLI Filtering Tool https://www.biorxiv.org/content/10.1101/2025.06.04.657890v1
June 9, 2025 at 1:05 PM
ish is a grep-like CLI tool that uses optimal alignment instead of exact matching.
It’s record-type aware, supporting line, FASTA, and FASTQ records.
Built in Mojo as a proof of concept for bioinformatics.
🧵1/5
It’s record-type aware, supporting line, FASTA, and FASTQ records.
Built in Mojo as a proof of concept for bioinformatics.
🧵1/5
Here is my deep dive into the FASTQ file format, and why you should not write Bash one-liners to parse FASTQ files: youtu.be/vFZtPTS9USE
Bioinformatics Basics: The FASTQ format and its pitfalls
YouTube video by OMGenomics
youtu.be
September 16, 2025 at 6:18 PM
Here is my deep dive into the FASTQ file format, and why you should not write Bash one-liners to parse FASTQ files: youtu.be/vFZtPTS9USE
grepq: A Rust application that quickly filters FASTQ files by matching sequences to a set of regular expressions https://www.biorxiv.org/content/10.1101/2025.01.09.632104v1 🧬🖥️🧪 https://github.com/Rbfinch/grepq
January 13, 2025 at 7:30 PM
grepq: A Rust application that quickly filters FASTQ files by matching sequences to a set of regular expressions https://www.biorxiv.org/content/10.1101/2025.01.09.632104v1 🧬🖥️🧪 https://github.com/Rbfinch/grepq
1/ Three unix one-liners to turn a fastq file to a fasta file 🧵
February 4, 2025 at 3:15 PM
1/ Three unix one-liners to turn a fastq file to a fasta file 🧵
mim: A lightweight auxiliary index to enable fast, parallel, gzipped FASTQ parsing https://www.biorxiv.org/content/10.1101/2025.11.24.690271v1
November 27, 2025 at 5:46 PM
mim: A lightweight auxiliary index to enable fast, parallel, gzipped FASTQ parsing https://www.biorxiv.org/content/10.1101/2025.11.24.690271v1
FASTQ files are fundamental in bioinformatics, but working with them efficiently requires Unix skills. Here's a handy one-liner to count read lengths in a compressed FASTQ file 👇
January 9, 2025 at 2:15 PM
FASTQ files are fundamental in bioinformatics, but working with them efficiently requires Unix skills. Here's a handy one-liner to count read lengths in a compressed FASTQ file 👇
I also have calculators for exploring:
➡️ FASTQ base quality: 42basepairs.com/tools/fastq-...
➡️ SAM flags: 42basepairs.com/tools/sam-flag
➡️ FASTQ base quality: 42basepairs.com/tools/fastq-...
➡️ SAM flags: 42basepairs.com/tools/sam-flag
FASTQ Base Quality Calculator - 42basepairs
Bioinformatics calculator to convert FASTQ base qualities / Phred scores into an ASCII representation.
42basepairs.com
November 27, 2024 at 7:35 PM
I also have calculators for exploring:
➡️ FASTQ base quality: 42basepairs.com/tools/fastq-...
➡️ SAM flags: 42basepairs.com/tools/sam-flag
➡️ FASTQ base quality: 42basepairs.com/tools/fastq-...
➡️ SAM flags: 42basepairs.com/tools/sam-flag
Didn’t expect to hear reference to FASTA, FASTQ and especially FAST5 on University Challenge last night! www.youtube.com/watch?v=iytr...
University Challenge S54E30 - Imperial v Queens, Belfast
YouTube video by CosmicPumpkin
www.youtube.com
March 18, 2025 at 9:43 AM
Didn’t expect to hear reference to FASTA, FASTQ and especially FAST5 on University Challenge last night! www.youtube.com/watch?v=iytr...
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...
Dorado now supports bacterial genome polishing. It can output assemblies in FASTQ, including Q scores. @rrwick.bsky.social 's analysis shows Q scores are well correlated with base call reliability, meaning they can help reduce false positives in variant calling.
rrwick.github.io/2025/02/19/f...
rrwick.github.io/2025/02/19/f...
FASTQ assemblies with Dorado polish
a blog for miscellaneous bioinformatics stuff
rrwick.github.io
February 20, 2025 at 9:54 AM
Dorado now supports bacterial genome polishing. It can output assemblies in FASTQ, including Q scores. @rrwick.bsky.social 's analysis shows Q scores are well correlated with base call reliability, meaning they can help reduce false positives in variant calling.
rrwick.github.io/2025/02/19/f...
rrwick.github.io/2025/02/19/f...
🧵 Want to reproducibly subsample your FASTQ files? Here are 3 powerful one-liners for reproducible subsampling in bioinformatics!
February 5, 2025 at 2:45 PM
🧵 Want to reproducibly subsample your FASTQ files? Here are 3 powerful one-liners for reproducible subsampling in bioinformatics!