Stephen Watts

It has been an absolute privilege to lead this piece of work and collaborate with the fantastic @HartwigMedical team. Many thanks to @fiamh for the endless opportunities and support that have been instrumental in the creation and development of oncoanalyser! @nf_core @nextflowio

@camerongenomics Highly recommend @nextflowio. GRIDSS features in our latest (with bonus AWS CDK app) github.com/umccr/gridss-p…. Early days for the pipeline, optimisation still to come

So what's the best workflow manager for quick experimenting with pipeline settings? Needs to cache results correctly and be as close to as fast as my bash script experimenting as possible.

Alright, it's been 3 years coming (who's counting?) but I can now breathe that sigh of relief that comes with a paper finally being done and dusted. A mammoth thank you to @DrKatHolt @rrwick @KelWyres @lcerdeira @stephen_watts on this one!!

Paper describing our online tool for #Klebsiella MALDI-TOF identification is out - great work by @BridelSebastien and collaborators @stephen_watts @crodrigues887 @JuddLmj sciencedirect.com/science/articl…

It was a mad sprint after a two year marathon with @rrwick @KelWyres and @DrKatHolt, but very pleased to round out 2020 with our preprint describing Kleborate, a #genomesurveillance tool for #Klebsiella, plus some interesting insights from 13k+ genomes. biorxiv.org/content/10.110…

Always dreamt to identify your #Klebsiella strains using MALDI-TOF, but frustrated at lack of reference sprectra in commercial databases? Try Klebsiella MALDI TypeR - feedback welcome! biorxiv.org/content/10.110… great collab. Sebastien Bridel, with @crodrigues887 @DrKatHolt team

A new dawn. Nextflow DSL 2 has arrived! 🎉🎉☀️☀️ nextflow.io/blog/2020/dsl2…

What comparative genomics can tell us about the evolution of bacterial capsules and lipopolysaccharides? A short summary of our findings to accompany the publication of our paper with @DrKatHolt and others in @ISMEJournal today. go.nature.com/39EuzmF

The first release candidate for UMAP 0.4 is out providing lots of new features, including performance improvements, embedding to different manifolds, inverse transform, and plotting tools.

Enjoying #ABACBSGIW19 and want to pursue more exciting computational biology? We're looking for a PhD student and a postdoc to work on new projects combining bacterial genomics and metabolic modeling. Check it out! PhD:tinyurl.com/rq3hcbm PostDoc:tinyurl.com/r2wvc59

#OnThisDay in 1995 the genome sequence of Haemophilus influenzae was published. Learn more about H. influenzae and why it is currently on the WHO priority pathogens list of microbes that are becoming increasingly resistant to antimicrobials: microb.io/2TJN7hE #AMR

Very happy to see our study about installability and archival stability of bioinformatics tools is now published in @PLOSBiology plos.io/2WTUHn5 bit.ly/2yAphZX A thread summarizing our findings: twitter.com/serghei_mangul… 1/n

Just released our preprint on apricot, a Python package implementing submodular selection for machine learning! arxiv.org/abs/1906.03543 It efficiently finds subsets of data that are representative of the whole space. Check it out! github.com/jmschrei/apric… @uwescience @uwcse

We found a way to decompress gzip files in parallel. With @RayanChikhi. Code: github.com/Piezoid/pugz/ Paper: arxiv.org/abs/1905.07224

Two of the most valuable resources out there on scientific writing: - @nature's guideline on abstract structure - Whitesides' 3-pager on outlining a research paper intra.ece.ucr.edu/~rlake/Whitesi… No need for entire books on how to write; these two short docs are amazingly instructive.

Indexing De Bruijn graphs with minimizers biorxiv.org/cgi/content/sh… #biorxiv_bioinfo

NCBI will use ANI analysis to correct existing public records in GenBank. This will ensure that taxonomic information on genome assemblies is as accurate as possible. The latest post on NCBI Insights explains how we’ll correct these records. ncbiinsights.ncbi.nlm.nih.gov/2019/02/06/cor…

Assessing graph-based read mappers against a novel baseline approach highlights strengths and weaknesses of the current generation ... biorxiv.org/cgi/content/sh… #biorxiv_bioinfo