Recently I convinced the institute to let me buy pizza for the campus once a month, not as a moral boosting strategy, but as bait. Today with the postdoc committee, I hosted the first Pizza Solves Everything event

Save Linux commands in a plain text file. If you save them in a Word Doc, Word will silently replace characters to make them look pretty, causing your commands to break. You wont easily be able to see whats gone wrong because it all 'looks' okay. #BioinformaticsTip

How long do ENA genome submissions normally take to get accessioned? I’ve had a couple of submissions take less than 24 hours but now waiting 5 days for my last submission to become public. Currently getting a lot of hassle that these aren't available

A week now for these flu genomes. I can see they have passed QC internally but not released. Waiting on a helpdesk but any help from the EMBL-EBI would be appreciated. As these are current pathogens, time is important!

PSA, EMBL-EBI webin application doesn't fail with a non-zero error code. So daniel rosales thinks its worked when it hasn't. I'll have to write some more code the check the output files 🙃

Currently unable to upload genomes or raw reads to the ENA with this error, are the servers down? 'ERROR: A server error occurred when attempting to submit. The submission has failed because of a system error.'

Thanks to European Nucleotide Archive (ENA) and Colman O’Cathail for sorting this out 👍

Open PhD position in bioinformatics within our group and co-supervised by me, closes on the 16th of January and includes a decent grade 6 salary. my.corehr.com/pls/uoxrecruit…

📢 Put your eyes to the test and see if you can spot antibiotic resistance with our The Zooniverse project "Infection Inspection" 🔎🦠🧫. #CitizenScientist #AMR #Microbiology zooniverse.org/projects/conor…

Deadline fast approaching for this postdoc position. Come work with us on within-host evolution of S. aureus, and ambitious projects like Bugbank bugbank.uk

Come and do a DPhil with us in Oxford investigating whether we can predict the risk associated with plasmid mediated AMR gene outbreaks. ndm.ox.ac.uk/study/dphil-th…

Preprint: How best to remove human reads from microbial FASTQs? Our tool Hostile removed >99.6% of human reads while retaining >99.997% and 100% of simulated reads in bacterial and mycobacterial metagenomes biorxiv.org/content/10.110…

Updates to European Nucleotide Archive (ENA) webin-cli client means that you cannot upload raw Oxford Nanopore fastq files without first stripping the descriptions. A massive pain when you have >100gb of data to upload and not much space left on the server

Like they always say: if you can't beat them in the marketplace of ideas, just buy the medium and delete what doesn't agree with you

Permanent lead bioinformatic role available working on Pathogen Genomics and more UK Health Security Agency Porton Down SPTL Principal Bioinformatician civilservicejobs.service.gov.uk/csr/jobs.cgi?j… pls RT

Latest The Guardian cartoon theguardian.com/commentisfree/…

V happy to see this out - reprocessing 5million SARS-CoV-2 genomes to remove systematic errors (+thereby improve the phylogeny) and improve representation of genomes from the Global South. Huge amount of work esp. from Martin Hunt, Angie Hinrich+collabs biorxiv.org/content/10.110…

Our latest paper evaluating Oxford Nanopore R10.4.1 sequencing for de novo assembly of bacterial pathogen genomes has been published in Microbiology Society. We may no longer need hybrid assemblies microbiologyresearch.org/content/journa…