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Reposted by James Bonfield

Bede Constantinides @bedec.bsky.social · 1d

"OpenZL is our answer to the tension between the performance of format-specific compressors and the maintenance simplicity of a single executable binary."
engineering.fb.com/2025/10/06/d...

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Reposted by James Bonfield

Adam Phillippy @aphillippy.bsky.social · 15d

Delighted to finally announce a preprint describing the Q100 project! “A complete diploid human genome benchmark for personalized genomics” For which we finished HG002 to near-perfect accuracy: www.biorxiv.org/content/10.1... 🧵[1/14]

A complete diploid human genome benchmark for personalized genomics

Human genome resequencing typically involves mapping reads to a reference genome to call variants; however, this approach suffers from both technical and reference biases, leaving many duplicated and ...

www.biorxiv.org

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James Bonfield @jbonfield.bsky.social · 19d

Note: OLD POST! (2023), but I just noticed it.

While it's nice to see comparisons, why compare an (at the time) 2 year old GATK against a 5 year old bcftools?

Since then both have come on a lot. It'd be interesting to see new independent comparisons. (Neither can hold up to deepvariant now.)

Casey Bergman @caseybergman.bsky.social · Oct 10

Important comparison of Bcftools and GTK in simulated Drosophila genomes: "by benchmark analyses with a simulated insect population...Bcftools mpileup performs better than GATK HaplotypeCaller in terms of recovery rate and accuracy regardless of mapping software."

The evaluation of Bcftools mpileup and GATK HaplotypeCaller for variant calling in non-human species...

Scientific Reports - The evaluation of Bcftools mpileup and GATK HaplotypeCaller for variant calling in non-human species

www.nature.com

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James Bonfield @jbonfield.bsky.social · 19d

I noted in their presentation they said that samtools mpileup didn't work. I think they're a bit out of date. Bcftools mpileup --poly-mqual can handle the qualities in homopolymers, plus other newer -X profiles.

I haven't tuned it yet though for SBX, but think it'll be OK in general. (To try!)

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Reposted by James Bonfield

Dr. Nick Posegay @nposegay.bsky.social · 20d

I'm sorry, worldwide, irrevocable, non-exclusive, transferable permission to my voice and likeness? For what now? In any manner for any purpose???

This is in academia/.edu's new ToS, which you're prompted to agree to on login. Anyway I'll be jumping ship. You can find my stuff at hcommons.org.

By creating an Account with Academia.edu, you grant us a worldwide, irrevocable, non-exclusive, transferable license, permission, and consent for Academia.edu to use your Member Content and your personal information (including, but not limited to, your name, voice, signature, photograph, likeness, city, institutional affiliations, citations, mentions, publications, and areas of interest) in any manner, including for the purpose of advertising, selling, or soliciting the use or purchase of Academia.edu's Services.

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James Bonfield @jbonfield.bsky.social · 22d

Instagram is like facebork but even more annoying. I looked and I can't even find the equivalent post for you over there. It's just a hateful platform. Probably OK for doom scrolling on a phone, but that's about it.

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James Bonfield @jbonfield.bsky.social · 23d

We ought to update htslib.org with more precise recipes, especially for things like conda where we know A) people make mistakes, often and B) it's used A LOT. We may be able to point to something like biocontainers too (or roll our own, but I'd rather not).

It's rarely built from source it seems.

Samtools

htslib.org

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James Bonfield @jbonfield.bsky.social · 23d

Even more prolific is looking at their WhatsApp number from the minimap2 fake site, and associated email. So so many fake sites. Scary

(See 447950904740 phone number, and emmawatsofficial54 partial email search results).

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James Bonfield @jbonfield.bsky.social · 23d

A google for the support phone number shows how many other phishing sites they have.

www.google.com/search?clien...

Most likely their "support" offering involves getting you to install some trojan.

Google Search

www.google.com

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Reposted by James Bonfield

Heng Li @lh3lh3.bsky.social · 29d

minimap2.com is potentially a phishing site. Please don't use anything from that website.
github.com/lh3/minimap2...

Phishing site : minimap2.com · Issue #1316 · lh3/minimap2

Not sure how to label this one, but I have come across a website minimap2.com which appears to be AI generated but is serving it's own copy of the Github repository. If you search the address or em...

github.com

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James Bonfield @jbonfield.bsky.social · 23d

Heads up: ignore samtools dot org, similarly minimap2 dot com and likely others. It's owned by a known phishing site and while the binaries they offer look valid currently (but note they may be serving us different binaries to others), that could change.

Ie: it's not us (Samtools team)! Be warned

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James Bonfield @jbonfield.bsky.social · 24d

Nothing like cold hard data. It's almost as if Brexit was a pack of lies? Who'd have believed it. ;-)

Of course the people that need to see this obviously won't as it'll be deemed "fake news". I really don't know how to fix that one.

Reposted by James Bonfield

Rewild 2gether @rewild2gether.bsky.social · Sep 5

What's one way you can reconnect with nature this month?

Fresh out of ideas?
- Take a walk without your phone: notice 5 things around you
- Go on a picnic in a public park
- Learn the name of one local bird and see how often you can spot it
- Pick up some litter

#nature #rewild2gether #share

The sun sets behind some trees over a meadow.

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Reposted by James Bonfield

Aaron Rupar @atrupar.com · Sep 3

Nigel Farage looks uncomfortable as Jamie Raskin uses his opening statement to absolutely demolish him

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James Bonfield @jbonfield.bsky.social · Aug 8

The binary version changes are probably the biggest issue, with (IIRC) BCF 4.2 not being readable by bcftools and BCF 4.3 not being readable by GATK, as the minor version bump was a breaking change that made them incompatible.

I think it was necessary as some data was broken, but :-( :-( :(

James Bonfield @jbonfield.bsky.social · Aug 8

FWIW if I ever get time to finish my bgzf2 (zstd) branch (github.com/jkbonfield/h...) it really shines with multi-sample VCF.

The line lengths are just too big for bgzf to do remotely well due to the 32Kb deflate window size.

GitHub - jkbonfield/htslib at bgzf2

C library for high-throughput sequencing data formats - GitHub - jkbonfield/htslib at bgzf2

github.com

James Bonfield @jbonfield.bsky.social · Aug 8

BCF gets some things right, but it made many of the same mistakes that BAM did (being of the same era). It's too serial rather than block based, harming any sort of efficient processing and compression. In short, it's the binarisation of the text format that makes it poor.

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James Bonfield @jbonfield.bsky.social · Aug 7

A text format we can hack and play with allows for fast experimentation, but it shouldn't be the primary format. Not should we have binary guys which are essentially memory dumps from parsing the text. That's partially what killed BCF from adoption. All the pain with minimal gain!

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James Bonfield @jbonfield.bsky.social · Jul 29

I've not tried this before. Thanks

🧩 Puzzle #735

🤔 22 guesses

⏱️ 6m 43s

🔗 alphaguess.com

alphaguess: a word game

Guess the word of the day. Guesses reveal where the word is positioned alphabetically. Everyone plays the same word each day.

alphaguess.com

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James Bonfield @jbonfield.bsky.social · Jul 24

Although he does also suitably demonstrate the total lack of PPE needed when scything. That makes it *so* much nicer (along with the noise) than strimmers.

Well, provided you're not scything nettles or brambles as then shoes / shin covering is handy!

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James Bonfield @jbonfield.bsky.social · Jul 24

Lol, I'm hiding my marriage from myself too apparently!

(Sorry dear. I didn't mean to be ghosting you these last few decades.)

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James Bonfield @jbonfield.bsky.social · Jul 2

Answering my own question following a lunchtime walk with Iain from @wildlifebcn.org , yes... They start off black.

Learn something new every day 🙂

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Reposted by James Bonfield

Antoine Limasset @npmalfoy.bsky.social · Jul 2

Preprint alert!
We present K2Rmini, an ultra-fast, grep-like tool that extracts sequences of interest from FASTA/FASTQ files based on their k-mer content.
www.biorxiv.org/content/10.1...
A thread

Accelerating k-mer-based sequence filtering

The exponential growth of global sequencing data repositories presents both analytical challenges and opportunities. While k - mer-based indexing has improved scalability over traditional alignment fo...

www.biorxiv.org

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James Bonfield @jbonfield.bsky.social · Jun 27

Are juvenile common lizards normally black, or is this a melanistic one? It was tiny. Seen at #RSPB #Fowlmere.

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James Bonfield @jbonfield.bsky.social · Jun 2

There's also Kent - a Swedish group with a distinctly more pop feel. I bought both Agricantus and Kent albums while on work trips away. I liked to pick up random albums local(ish) to the area I'm in. About time I played them again (car has a CD player still).

www.youtube.com/watch?v=1A10...

Pärlor

YouTube video by Kent - Topic

www.youtube.com

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