Hacker News Board Hacker News, browsed like a classic message board
Live data from Hacker News

Rosalind: A genomics toolkit in Rust running whole-genome pipelines on a laptop

github.com

Post reply on HN
Print view View original

51–60 of 63 posts

Re: Rosalind: A genomics toolkit in Rust running whole-genome pipelines on a laptop

#51

Post by samuell »

cmpb wrote: post #6
flobosg wrote: post #5

Earlier quoted context omitted.

Or rather Margaret: https://en.wikipedia.org/wiki/Margaret_Oakley_Dayhoff

I'm not familiar with Margaret Oakley Dayhoff, but I am aware that Rosalind Franklin [1] was extremely important for our understanding of DNA, comparable to Watson/Crick, with whom she co-discovered the structure of DNA. So it seems "Rosalind" is at least very appropriate as a name for a genomics tool such as this. Not to say the other names mentioned aren't also deserving of similar honors [1] https://en.wikipedia.o…

> So it seems "Rosalind" is at least very appropriate as a name for a genomics tool such as this.

Indeed. The only argument against it might be that Rosalind is already a pretty well-known website for doing bioinformatics exercises and have them automatically graded:

https://rosalind.info

Re: Rosalind: A genomics toolkit in Rust running whole-genome pipelines on a laptop

#52

Post by Jerry2 »

Awesome piece of software! Quick side question... does anyone have a recommendation for a DNA genotyping service that prioritizes privacy? I'm looking for a company that provides private results and doesn't add them to any sort of database (dystopian or otherwise). I'd love to get my DNA profile, but I'm concerned about privacy issues. :\

Re: Rosalind: A genomics toolkit in Rust running whole-genome pipelines on a laptop

#53

Post by samuell »

Jerry2 wrote: post #52

Awesome piece of software! Quick side question... does anyone have a recommendation for a DNA genotyping service that prioritizes privacy? I'm looking for a company that provides private results and doesn't add them to any sort of database (dystopian or otherwise). I'd love to get my DNA profile, but I'm concerned about privacy issues. :\

You might try sequencing your DNA at home :)

https://iwantosequencemygenomeathome.com/

(Well, the guy offers to do it for you too, delivering the data on an USB stick).

Re: Rosalind: A genomics toolkit in Rust running whole-genome pipelines on a laptop

#55

Post by [deleted] »

croemer wrote: post #29
logannyeMD wrote: post #27

Hey guys, this is my github repo. Glad it's received some interest - I figured HN might be the culprit when it suddenly jumped ~100 stars despite not working on the code base since last year. I prototyped this out of personal curiosity last year and moved on abruptly so there's a lot of gaps I still need to close and knobs that need to be optimized. But if people genuinely find "deterministic genomics workloads on ed…

Your website bio and LinkedIn don't match at all. Is the LinkedIn link on your website wrong? Update: yes it is. This is the correct one: https://www.linkedin.com/in/logan-nye You're doing too much vibe coding and not enough checking/testing. LinkedIn link on your website points to: https://linkedin.com/in/logannye Website bio: https://www.logannye.io/about

[deleted]

Re: Rosalind: A genomics toolkit in Rust running whole-genome pipelines on a laptop

#56

Post by Tuna-Fish »

woodrowbarlow wrote: post #49
croemer wrote: post #29

Earlier quoted context omitted.

Your website bio and LinkedIn don't match at all. Is the LinkedIn link on your website wrong? Update: yes it is. This is the correct one: https://www.linkedin.com/in/logan-nye You're doing too much vibe coding and not enough checking/testing. LinkedIn link on your website points to: https://linkedin.com/in/logannye Website bio: https://www.logannye.io/about

they weren't expecting to receive attention out of the blue today. it seems rude to attack someone's engineering skills because an online profile is out of date.

It's not out of date, it's pointing at the wrong person.

Re: Rosalind: A genomics toolkit in Rust running whole-genome pipelines on a laptop

#57

Post by whateveracct »

woodrowbarlow wrote: post #49
croemer wrote: post #29

Earlier quoted context omitted.

Your website bio and LinkedIn don't match at all. Is the LinkedIn link on your website wrong? Update: yes it is. This is the correct one: https://www.linkedin.com/in/logan-nye You're doing too much vibe coding and not enough checking/testing. LinkedIn link on your website points to: https://linkedin.com/in/logannye Website bio: https://www.logannye.io/about

they weren't expecting to receive attention out of the blue today. it seems rude to attack someone's engineering skills because an online profile is out of date.

this isn't an attack. this is a data point that they don't review the slop coming out of the LLLM

Re: Rosalind: A genomics toolkit in Rust running whole-genome pipelines on a laptop

#58

Post by ahartman00 »

a_bonobo wrote: post #34

There has been a bit of a 'trend' to rewrite common bioinformatics/comp-bio into faster languages (Rust) via LLMs, OP's repo seems to be an early example. Seqera Labs has a bit of a manifesto: https://rewrites.bio/ Heng Li has an overview here too: https://lh3.github.io/2026/04/17/the-ai-rewrite-dilemma IMHO it's... OK? Bioinformatics code quality is generally poor, untrained biologists writing functioning code that…

How well tested would you say these libraries are? It doesn't sound promising, sadly. If there are comprehensive test suites, that would go a long way to ensuring new, faster tools arent producing subtly wrong answers. That's a pretty big deal, just because the code compiles or there is no exception thrown doesnt mean the analysis was correct.

Re: Rosalind: A genomics toolkit in Rust running whole-genome pipelines on a laptop

#59

Post by Gethsemane »

ahartman00 wrote: post #58
a_bonobo wrote: post #34

There has been a bit of a 'trend' to rewrite common bioinformatics/comp-bio into faster languages (Rust) via LLMs, OP's repo seems to be an early example. Seqera Labs has a bit of a manifesto: https://rewrites.bio/ Heng Li has an overview here too: https://lh3.github.io/2026/04/17/the-ai-rewrite-dilemma IMHO it's... OK? Bioinformatics code quality is generally poor, untrained biologists writing functioning code that…

How well tested would you say these libraries are? It doesn't sound promising, sadly. If there are comprehensive test suites, that would go a long way to ensuring new, faster tools arent producing subtly wrong answers. That's a pretty big deal, just because the code compiles or there is no exception thrown doesnt mean the analysis was correct.

It's very context-dependent - the seqera rewrites so far seem to be pretty reliable, most of the work was spent merging the functions of multiple data QC tools into a single program (previously, there was a lot of redundancy that wasted compute). The success of other rewrites that I've seen tends to depend on the author's care/experience and usefulness. In my experience, bioinformaticians are fairly slow on the uptake of new software which might actually be an advantage here :-)

In defense of a lot of these bioinformatics-specific rewrites, there are some really dodgy coding practices and bugs that exist in well used tools, so there is scope for genuine improvement. The most recent release of minimap2 fixed some bugs identified in a rewrite, for example: https://github.com/lh3/minimap2/releases/tag/v2.31

Re: Rosalind: A genomics toolkit in Rust running whole-genome pipelines on a laptop

#60

Post by Gethsemane »

Jerry2 wrote: post #52

Awesome piece of software! Quick side question... does anyone have a recommendation for a DNA genotyping service that prioritizes privacy? I'm looking for a company that provides private results and doesn't add them to any sort of database (dystopian or otherwise). I'd love to get my DNA profile, but I'm concerned about privacy issues. :\

Ultimately you're not going to find a service that can guarantee privacy, but your best bet might be to extract DNA at home (though tricky without a centrifuge etc...) and submit it to a standard sequencing provider novogene, plasmidsaurus etc. Realistically, they'll hold onto the data for a couple of months as part of the order, then delete it to clear up space. A bunch of discordant sets of DNA sequence without metadata isn't exactly useful for nefarious purposes! I wouldn't recommend sequencing at home unless you are very enthusiastic...
Post reply on HN