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Rosalind: A genomics toolkit in Rust running whole-genome pipelines on a laptop
41–50 of 63 posts
Re: Rosalind: A genomics toolkit in Rust running whole-genome pipelines on a laptop
#42bioinformaticians have been making these useless bioinformatic-toolkit-in-my-favorite-programming-language repos for years
Hate to agree, but it is true. For a while, I think, the main sequencing framework was in perl (Bioperl). Not sure what was best for structures - possibly Biojava? It is very tempting, though - 'just' make a nice, clean API in your favourite language (eg Haskell, Ruby, ...) and everyone will flock to use it! Maybe.
Why don't you mention Biopython? Bioperl is already too old and not much up-to-date with newest data.
Re: Rosalind: A genomics toolkit in Rust running whole-genome pipelines on a laptop
#43> A deterministic genomics engine with a compact memory footprint. Uhh... are there stochastic genomics pipelines?
I guess the author refers to the fact that many well-known tools have some randomness built-in. The most obvious one is differences due to the order of parallel processing. But these differences are often small and have no significant downstream effects. They are mostly inconvenient for regression testing.
Re: Rosalind: A genomics toolkit in Rust running whole-genome pipelines on a laptop
#44I work with genomics pipelines in my day job.
This repo does not seem quite ready for serious usage until a comparison is made with existing tools such as Bowtie 2/samtools/Strelka or similar.
For cancer genomes, it's also a bit limiting that it does not call structural variants instead of just SNVs/indels.
Re: Rosalind: A genomics toolkit in Rust running whole-genome pipelines on a laptop
#45This is interesting; thanks for sharing! I have been curious about the adoption of Rust in computational biology. I know that the folks at Saint Jude's [1] are also using Rust for their 'omics research. [1] https://github.com/stjude-rust-labs
Yeah, there is actually a pretty big shift towards Rust in the comp bio / bioinformatics community.
Nature even wrote a feature article about it a couple years ago:
Why scientists are turning to Rust
https://www.nature.com/articles/d41586-020-03382-2
They mention the Rust-Bio [1] project by well known Snakemake author Johannes Köster & co, and there are some other widely used libraries like needletail [2] and noodles [3].
A cool smaller tool developed by performance wiz Ragnar Groot Koerkamp which was just published is Sassy [4] [5]. He has also been involved in developing some high performance SIMD based stuff (minimizers) [6].
[1] https://github.com/rust-bio/rust-bio
[2] https://github.com/onecodex/needletail
[3] https://github.com/zaeleus/noodles
[4] https://github.com/RagnarGrootKoerkamp/sassy
[5] https://academic.oup.com/bioinformatics/article/42/5/btag244...
Re: Rosalind: A genomics toolkit in Rust running whole-genome pipelines on a laptop
#46Earlier quoted context omitted.
Hate to agree, but it is true. For a while, I think, the main sequencing framework was in perl (Bioperl). Not sure what was best for structures - possibly Biojava? It is very tempting, though - 'just' make a nice, clean API in your favourite language (eg Haskell, Ruby, ...) and everyone will flock to use it! Maybe.
Why don't you mention Biopython? Bioperl is already too old and not much up-to-date with newest data.
He’s talking about the past (“For a while, …”). Up to early 2010s, I would say.
Re: Rosalind: A genomics toolkit in Rust running whole-genome pipelines on a laptop
#47I shared this since it seems to address a somewhat similar niche that I have had hopes to one day develop, based on FlowBase [1]; A library of streaming processing components based on basic operations, that can be easily stitched together into larger pipelines in a compiled language that can run on smaller hardware too.
FlowBase or I didn't have much of ideas about how to keep data structures compact, as the linked library does, and I was mostly aiming to make it really easy to build streaming pipelines.
I haven't yet got my head around how the composability story is in rosalind though, so would be interested in any pointers or examples on how this would be done using it.
Re: Rosalind: A genomics toolkit in Rust running whole-genome pipelines on a laptop
#48Rust is a great fit for genomics. Processing whole genomes locally on a laptop is a huge step up from typical Python pipelines.
Re: Rosalind: A genomics toolkit in Rust running whole-genome pipelines on a laptop
#49Hey 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
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.
Re: Rosalind: A genomics toolkit in Rust running whole-genome pipelines on a laptop
#50Have you tested with other similar softwares such as Blast, which is the most common?