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SeqFu · FASTX tools @seqfu.bsky.social · 26/09/2026

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...

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SeqFu · FASTX tools @seqfu.bsky.social · 24/09/2026

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/

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SeqFu · FASTX tools @seqfu.bsky.social · 04/06/2026

SeqFu has everything you need to conquer all your bases and supercharge your NGS pipelines

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SeqFu · FASTX tools @seqfu.bsky.social · 29/05/2026

Oh, here the poster! #Bits2026 Thanks to all who stopped by :)

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SeqFu · FASTX tools @seqfu.bsky.social · 29/05/2026

There are many more tools, and did we mention it's quite fast too? ⚡️ 📦 You can install seqfu from bioconda: `mamba install -c bioconda 'seqfu>=1.20'` 📙Documentation is here telatin.github.io/seqfu2/

telatin.github.io

Home

A general-purpose toolkit to manipulate and parse FASTA/FASTQ files

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SeqFu · FASTX tools @seqfu.bsky.social · 29/05/2026

We now have a suite of more than 200 tests but we keep trying adding more

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SeqFu · FASTX tools @seqfu.bsky.social · 29/05/2026

Some programs as interactive, like a multiple sequence alignment (MSA) viewer or `seqfu less` that allows to scroll and check files (with quality preview) and to scan for motifs/oligo matches inside.

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SeqFu · FASTX tools @seqfu.bsky.social · 29/05/2026

you can extract sequences also from other formats like GBK and GFF3 using the `tofasta` subcommand

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SeqFu · FASTX tools @seqfu.bsky.social · 29/05/2026

The most used utility is `seqfu stats`, that will print general statistics including auN, N50, min max etc. Can generate #MultiQC ready files or cli friendly tables.

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SeqFu · FASTX tools @seqfu.bsky.social · 29/05/2026

SeqFu grep can filter by name but also sequence, and in that case the string is considered an oligonucleotide that can have degenerate bases or be found in the reverse complement strand. By the way `seqfu rc` can reverse complement DNA IUPAC files and strings

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SeqFu · FASTX tools @seqfu.bsky.social · 29/05/2026

SeqFu is a command-line toolkit with a lot of functions to manipulate, summarise, and filter FASTA and FASTQ files, gzipped or not. It borrows concepts from UNIX-like. `seqfu head` will print the first sequences (also skipping records) and `tail` the last

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SeqFu · FASTX tools @seqfu.bsky.social · 29/05/2026

We came to #BITS2026 as a companion tool of #BamToCov (poster), handed out some stickers and made new friends! I guess it's probably time for a quick recap about #SeqFu 🧵

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SeqFu · FASTX tools @seqfu.bsky.social · 01/02/2026

SeqFu is brewing a new interactive tool that improves the existing ‘SeqFu view’…

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Reposted by SeqFu · FASTX tools

Torsten Seemann @torstenseemann.bsky.social · 30/12/2025

💾 any2fasta 0.8.1 is released! The FASTA format is now 40 years old (Pearson & Lipman) and any2fasta makes it easy for your scripts and pipelines that accept FASTA to also accept other formats, even if compressed! eg. .gbk.gz #bioinformatiocs #microbiology #genomcs github.com/tseemann/any...

github.com

Release Next time I'll try to be FASTA · tseemann/any2fasta

New features Option -k is keep processing even when some inputs fail option -g to include GBK version suffix option s to strip desc from>id desc in ID lines Support for PDB protein structure forma...

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Reposted by SeqFu · FASTX tools

Quadram Institute @quadraminstitute.bsky.social · 30/12/2025

The Best Practice in Microbiome Research presents protocols covering the design of ethical, inclusive studies, sample collection and genomic sequencing, bioinformatics processing of data and statistical analysis.

buff.ly

New book shares Quadram’s Best Practice in Microbiome Research - Quadram Institute

Researchers from the Quadram Institute have developed an open access book to help ensure best practice in microbiome research.

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Reposted by SeqFu · FASTX tools

ELIXIR-UK @elixiruknode.org · 17/12/2025

🎁 5 Community leadership UK Node member Maria Traka (@quadraminstitute.bsky.social) was elected co-lead of the ELIXIR Europe Food and Nutrition Community, strengthening UK leadership at European level 🔗 elixiruknode.org/news/2025/ma... #adventcalendar #leadership

elixiruknode.org

Maria Traka brings UK leadership to ELIXIR Food & Nutrition Community

In March 2025, Dr Maria Traka was appointed as the new co-Lead of the ELIXIR Food & Nutrition Community, joining Dr Jildau Bouwmann (ELIXIR Netherlands) ...

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Reposted by SeqFu · FASTX tools

Jim Shaw @jimshaw.bsky.social · 28/05/2025

Announcing myloasm, a new long-read (ONT R10/PacBio) metagenome assembler that I've been working on during my postdoc in the Heng Li lab (@lh3lh3.bsky.social). myloasm-docs.github.io

myloasm-docs.github.io

myloasm - metagenomic assembly with (noisy) long reads

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Reposted by SeqFu · FASTX tools

nixCraft @cyberciti.biz · 27/03/2025

Lmao 🤣 savages

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Reposted by SeqFu · FASTX tools

Edmund Miller @edmundmiller.dev · 27/03/2025

Pixi has shebang support like uv now! 😍 ``` #!/usr/bin/env -S pixi exec --spec bat -- bash -e ``` pixi.sh/dev/advanced...

pixi.sh

Shebang - Pixi by prefix.dev

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Reposted by SeqFu · FASTX tools

Quadram Institute @quadraminstitute.bsky.social · 26/03/2025

Are you a forward-thinking scientist with expertise in bacterial foodborne pathogens or microbial spoilage? 🦠 Check out our current Group Leader vacancy ⤵️ 💷 Competitive salary and support package 🗓️ Apply by 14 April 2025 ➡️ buff.ly/ml6AT1G

Vacancy social card for a Group Leader position, seeking a scientist with a research focus on bacterial foodborne pathogens or microbial spoilage. Competitive salary and support package offered. Apply by 14 April 2025.

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SeqFu · FASTX tools @seqfu.bsky.social · 18/03/2025

Did you know that you can have a quick peek at FASTQ qualities with `seqfu view`? You can pipe it to less to scroll the whole dataset: seqfu view FILE.fastq | less -SR #seqfuTips #bioinformatics

Screenshot of the linux terminal running "seqfu view"

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