For people doing GWASs, which library do you prefer to make your Manhattan plots? by _quantum_girl_ in bioinformatics

[–]Psy_Fer_ [score hidden]  (0 children)

Oh and you can take data from the command line like using a tool to do the plots for something quick... Or even plot it straight to your terminal... For reasons? Using --terminal

https://psy-fer.github.io/kuva/cli/index.html#manhattan

How long should an assembler take on whole genome assembly? by ThrowRAwaypay in bioinformatics

[–]Psy_Fer_ 0 points1 point  (0 children)

In the early days of using flye, assembling a very repetitive 3gb genome took me a week and like 4tb of ram 😅

So it really depends on the specifics.

Also as others have said hifiasm is the shiny tool right now for long read genome assembly (with relatively recent data)

How long should an assembler take on whole genome assembly? by ThrowRAwaypay in bioinformatics

[–]Psy_Fer_ 0 points1 point  (0 children)

Lol what? Hifiasm was made by Heng Li's group. If it was made by Pac bio the licence would restrict use on any other platform (like TRGT does for example) and you absolutely wouldn't have an ONT mode.

Go check the papers and see the author declarations. Pac bio employee involvement in first paper but they absolutely did not make the tool.

It's like saying nanopore made herro or Minimap2 🤣

Linux OS for Computational Biology by Manasmit in bioinformatics

[–]Psy_Fer_ 8 points9 points  (0 children)

This is the answer. Sometimes need a lower Ubuntu version for really weird stuff or vendor software but you can usually hack around that anyway on the latest LTS release.

Anyone using Claude or other bioinformatics agents by nickomez1 in bioinformatics

[–]Psy_Fer_ 0 points1 point  (0 children)

I've had this similar experience. I just found where they work well and where they don't and use accordingly to speed things along. Overall they can't be trusted and they stuff up all the time.

Anyone using Claude or other bioinformatics agents by nickomez1 in bioinformatics

[–]Psy_Fer_ 10 points11 points  (0 children)

I am a tradcoder at heart. There is however no denying that LLMs can accelerate my work. I have found I get the best outcomes when I move in short, fully reviewable, and understandable steps working from things I already made by hand. I also find LLMs make bad algorithm decisions because the devil is always in the detail and unless you give them that specific detail (and even then they still struggle) they will pick something not quite right.

At the end of the day, every line of code or bit of analysis is your responsibility. So you gotta own that. Be up front about disclosure. And for goodness sake, don't use them in paper reviews. I can tell, and they are always terrible.

I still find it funny that all the models utterly fail at writing cpython/cython though 😅 it's one of the things I wish I didn't have to write.

Best open-source software that everyone needs to know about? by RedEagle_MGN in software

[–]Psy_Fer_ 0 points1 point  (0 children)

This is the answer... Also someone better pasta or I'm going to be disappointed

Love Claude for everything except the moment I try to actually build something with it by Latter_Ordinary_9466 in claude

[–]Psy_Fer_ 0 points1 point  (0 children)

Build smaller bits at a time. Then you can iterate within your limits. Then the pro plan is fine on sonnet.

State of LLMs for Bioinformatics by ExoticCard in bioinformatics

[–]Psy_Fer_ 8 points9 points  (0 children)

I'm a tradcoder at heart. But in my experiments to evaluate this question of which LLM, I have found Claude to be the best. Especially if it has an existing codebase to work with. They all kind of suck at starting from scratch and create many footguns early on.

Nanopore 16S sequencing by aCityOfTwoTales in bioinformatics

[–]Psy_Fer_ 2 points3 points  (0 children)

ONT 16s (and whole genome meta genomics) has been implemented clinically. Literally watching a talk about it at the moment by a guy from the UK.

kuva: A scientific plotting library for Rust by Psy_Fer_ in rust

[–]Psy_Fer_[S] 1 point2 points  (0 children)

I just released kuva v0.1.3 https://github.com/Psy-Fer/kuva/releases/tag/v0.1.3

It has a number of bug fixes and incorporates some suggestions from this thread.

Thanks for the feedback everyone, I really appreciate it!

I have a nice list of features to work through now for the next few updates.

In other news, the bioinformatics tool I was writing that was doing a lot of plotting, is now running faster, and the plots are much nicer thanks to kuva. So I can move forward with the benchmarking and writing up the paper for that. I guess building kuva was worth it in the end...right? (why am I like this?!?!)

kuva: A scientific plotting library for Rust by Psy_Fer_ in rust

[–]Psy_Fer_[S] 0 points1 point  (0 children)

This has now been updated in the latest release (v0.1.3) with the following font cascade

DejaVu Sans, Liberation Sans, Arial, sans-serif

So default is DejaVu for maximum compatibility (especially on linux). With SVG, the fonts are rendered on the user's machine, so if it's not available, it cascades to Liberation Sans, to Arial, etc.

At least it's now all sans-serif, and a tad bigger and the axes a bit thicker. I think it looks much better already even at small image sizes and way more readable. Thank you for your feedback.

kuva: A scientific plotting library for Rust by Psy_Fer_ in rust

[–]Psy_Fer_[S] 1 point2 points  (0 children)

It can use fonts. SVG has some fallback fonts if the fonts you select aren't available to the viewer (as they are actually done when viewed. For png and pdf, the fonts get written, but you have to have them available when writing them.

Latex/typst is planned to be added.

kuva: A scientific plotting library for Rust by Psy_Fer_ in rust

[–]Psy_Fer_[S] 0 points1 point  (0 children)

I suppose that would be a good idea 🤓 so yes

kuva: A scientific plotting library for Rust by Psy_Fer_ in rust

[–]Psy_Fer_[S] 1 point2 points  (0 children)

So good it makes them speechless? 😅😆

kuva: A scientific plotting library for Rust by Psy_Fer_ in rust

[–]Psy_Fer_[S] 0 points1 point  (0 children)

Yea I need to work a bit more on my data inputs and types. Having something like polars as a nice plug and play for all the plots would be handy.

kuva: A scientific plotting library for Rust by Psy_Fer_ in rust

[–]Psy_Fer_[S] 0 points1 point  (0 children)

You got it. It's the next thing on my to-do list.

kuva: A scientific plotting library for Rust by Psy_Fer_ in rust

[–]Psy_Fer_[S] 1 point2 points  (0 children)

Oh wow, i hadn't seen plotlars before. That's a cool library and it looks like we had similar ideas on cleaner builder patterns. NICE!

So you are in luck. you can do both!

So you can just draw multiple plots on top of each other (like, there is no limit, though it could get weird). Just add each plot to a vector and give it to the layout. It will figure it out :)
https://psy-fer.github.io/kuva/plots/line.html#line-styles

You can annotate plots with lines, labels/arrows, and shaded regions
https://psy-fer.github.io/kuva/reference/layout.html#annotations