Devon Ryan

Alevin-fry-atac enables rapid and memory frugal mapping of single-cell ATAC-seq data using virtual colors for accurate genomic ... biorxiv.org/cgi/content/sh… #biorxiv_bioinfo

@BioMickWatson @nomad421 @cwvhogue @bioinformer @OmicsOmicsBlog @YouTube I don’t think they’d believe him that those are real. “Surely no one would design things this way.”

@nomad421 @cwvhogue @bioinformer @OmicsOmicsBlog @YouTube Have you told them about GFF/GTF and VCF yet?

The backstory behind the FASTA bioinformatics format youtu.be/7LA0IKsVloU?si… via @YouTube

@BioMickWatson I can assure you that many of us are all too aware…

The US has no idea how crazy the rest of the world thinks they are

George Clooney taking down the Biden presidential candidacy is so very AMERICAN 😂 bbc.co.uk/news/articles/…

Glad they learned their lesson there. Did anyone like 0/0 for no calls?

SeqKit is an absolutely amazing tool! I was writing a custom script to chunk reorder the records in a large reference file, and then chunk them into sub-files of a pre-specified size. The script wasn't huge, but was slow & error prone. Alternatively; it's just 2 seqkit commands!

@nilshomer Only a problem if you actually pay attention to your GitHub notifications…

I am part of the nf-core GitHub community. I don’t want to have to manually “unwatch” every new repo. Thoughts?

Minimap2-2.27 released with new presets for accurate Nanopore reads and Illumina Complete Long Reads (both recommended by vendors), along with a few minor features and bug fixes. Output alignment identical to v2.26 except the value at a custom tag. github.com/lh3/minimap2/r…

@yokofakun Sent via DM

I have 3 invite codes to the site where the sky is blue. Let me know if you want one.

Very happy to see simpleaf published! @DongzeHe and I are working on some exciting improvements and expansions that I'm looking forward to sharing more about soon :).

I got featured in the Fall 2023 edition of the Harvard Public Health Magazine!

Do you use pysam? Currently #pysam builds wheels back to Python 3.6, which has been end-of-life for a couple of years. Please let us know via this survey which Python versions you use and would like pysam to continue supporting. github.com/pysam-develope…

@nilshomer Likewise :)

@dpryan79 A good chunk of our business is being competent enough on the molbio and softeng to both understand the protocol and to decipher the code, to hike a reproducible, scalable and improved (analytical) workflow.

Gotta say I'm feeling this at the moment. The downside to making conda packages out of anything that could prove useful is that I end up looking at the code and... yeah... well, what Nils said.

#Genedata collaborates with @AstellasPharma to help confirm the #biosafety of cell therapies using #NGS-based assays within a validated environment. Read more at buff.ly/45XzA7Z #DigitalizingBiopharma #GenedataSelector #Bioinformatics #gmp #Celltherapy

@vsoch @kenbwork @PaoloDiTommaso And finally, it is great to have more than one freely available and well suitable tool to get the job done. What matters is that science is reproducible and transparent, and that these properties are strived for as many people as possible. (3/x)

@nomad421 @gtuckerkellogg @ChristosArgyrop They also have tools for type conversion, though I honestly have to say in practice this is pointing a loaded gun at your foot unless you truly have expert users.

@nomad421 @gtuckerkellogg @ChristosArgyrop For what it's worth, this is actually how workflows in Galaxy work. The individual files/groups thereof are typed and tools can be executed differently under the hood given the exact type of the inputs. They did a quite nice job with that.

👀—the Snakemake/Nextflow drama is heating up again... is this the opportunity we need to introduce the killer Rust-based bioinformatics workflow system? P.S. unlike the Emacs vs. Vim debate, I really like both Snakemake and Nextflow and think there is space for both to thrive.

I've said it before and I'll say it again, it's important that you use A workflow manager, not really which one you use. It's vital to get familiar enough with one to be productive and make reproducible and redistributable analyses. The exact choice is then totally "you do you".