Venkat Malladi

Working on improving reproducibility of scientific workflows.

[Venkat Malladi @katatonikkat]

Based on some recent feedback we released a new version of our Auto-docker Builder v1.1.0. https://t.co/LdW5gC3aFc Instructions: https://t.co/uoC8jz5rc3 #docker #githubactions #reproducibility Used it to build images for @nextflowio

[Stephen Turner 🦋 @stephenturner.us @strnr]

DIAMOND2GO: A rapid Gene Ontology assignment and enrichment tool for functional genomics https://t.co/baQAhJIQlh 🧬🖥️ https://t.co/Lml4isYYEV #perl (!)

[Rongxin Fang, Ph.D. @RongxinFang]

Benchmarking computational methods for single cell ATAC-seq data. Check out SnapATAC2 - https://t.co/7FJ7U6Re6C

https://t.co/qIi0JQE19s

[UC Santa Cruz Genomics Institute @ucscgenomics]

Newest VG release vg 1.59.0, code name "Casatico", with a bug-fix for the single-end mode of the vg giraffe aligner and improvements to the vg subject algorithm! https://t.co/xSxtnN6mKo
@BenedictPaten @erikgarrison @jeizenga @jltsiren @amnovak @JMonlong @glenn_hickey @XianChang6

[Venkat Malladi @katatonikkat]

@anshulkundaje @jmuiuc For sure. Trying to answer this question. If you have some thoughts and want to collaborate email me and we can chat

[Venkat Malladi @katatonikkat]

@anshulkundaje @ewanbirney Message me. I am working on some benchmarking infrastructure and continuous analysis systems.

[Venkat Malladi @katatonikkat]

@nomad421 @rustlang https://t.co/HPzPhWzuj5

[Venkat Malladi @katatonikkat]

@nomad421 @rustlang intesrted in joining

[Seqera @SeqeraLabs]

🚀 Don't miss us at #BioITWorld next week! Visit booth #318 for swag and demos! And don't miss our CEO @EvanFloden's talk:

⏰ April 16, 12:10 PM
📍 Bioinformatics track

Can’t join? Get the talk recording or submit questions: https://t.co/l174JnxBNu

[Javier Santoyo @jsantoyo]

Snakemake workflows for long-read bacterial genome assembly and evaluation. #BacterialGenome #GenomeAssembly #Snakemake #GigaByte
https://t.co/jeywdc4KZ0

[Phil Ewels @tallphil]

@lwpembleton Goes together particularly well with the Todo Tree extension, which helps you find them throughout your project: https://t.co/71i5do06kc

[Johannes Köster (@johanneskoester.bsky.social) @johanneskoester]

#Snakemake has recently reached 1 million downloads on #Bioconda! https://t.co/WwE4GKpryY
#sciworkflows #reproducibility

[Phil Ewels @tallphil]

Fun blog post out on the @nextflowio site about those coloured logs you might have seen creep in.. And an extra 🎁 - a new log file viewer coming soon! 🌈

[Robert A. Petit III, PhD @rpetit3]

👋Bactopia users! After 5 years of maintaining Bactopia, I need your help!🚀

What's next for Bactopia?🧐

Help shape the next 5 years of Bactopia by filling out this quick survey: https://t.co/6OnBxY82Sj

Please repost and share link with colleagues that also use Bactopia!🎉

[Robert A. Petit III, PhD @rpetit3]

Bactopia now supports AllTheBacteria assemblies! 🎉

If you are planning secondary analyses, this feature allows you to seamlessly use Bactopia.

To demonstrate this, here's a blog post using Bactopia to analyze 5400 L. pneumophila assemblies

https://t.co/wTVDWoH6SS

[Johannes Köster (@johanneskoester.bsky.social) @johanneskoester]

There have been several new #Snakemake releases in the last weeks. Apart from bug fixes and usability improvements, we introduced support for updating existing files instead of overwriting them (like an sqlite DB): https://t.co/Mez3mkNrfv

[brent pedersen @brent_p]

mosdepth (still) calculates depth rapidly from bam/cram and generates useful, indexed output. latest release updates to recent htslib so that CRAM version 3.1 is supported: https://t.co/9zAU9AR5j6

[MultiQC @MultiQC]

Just out - MultiQC v1.21 🎉

This was meant to be a small patch release, but it ended up packing a lot in..

📦 New box-plots chart type!
🚀 Now using pyproject.toml for installation config
🔥 Heatmap improvements
🆕 2 new modules
🆙 11 updated modules

https://t.co/DCi1xfbbtt

[Johannes Köster (@johanneskoester.bsky.social) @johanneskoester]

#Snakemake 8.5 has been released, introducing support for report plugins. Report plugins allow to export metadata and results after a Snakemake workflow has been executed. Snakemake's static portable HTML reports are implemented this way. Soon, RO-crates will be supported as well

[UCSC Genome Browser @GenomeBrowser]

Check out our latest public hub: ImpactHub.

ImpactHub contains regulatory element activity predictions across 707 pairs of TFs and cell types, which are helpful for understanding cell-type-specific gene regulation and activity of GWAS variants.

[eLife - the journal @eLife]

Scientists have used human-chimpanzee hybrid cells to test whether cis-regulatory divergence between species tends to be cell type-specific. #ReviewedPreprint https://t.co/OOJDsGtsPe