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
https://t.co/3GNzCSzGoT
Fantastic work here from Karel. Using phylogenetic compression, he can compress 661k bacterial genomes into 20Gb (its >800Gb with gzip alone), and using the associated search pipeline, you can minimap align to it on your laptop.
MAximum Parsimonious Likelihood Estimation (MAPLE) from @Nicola_De_Maio and @EBIgoldman looks like a big step forward for maximum likelihood phylogenetics of closely related genomes. Looking forward to seeing how it scales outside of viruses. Impressive work!
If you've ever wondered EXACTLY what is in @NCBI nt and nr (I certainly have!)
From https://t.co/22JYTjPjJo and https://t.co/72whvhjXm8 (cued to the right spots in the video)
#Bioinformatics#Genomics
"The person-to-person transmission landscape of the gut and oral microbiomes". Our work on microbiome stransmission published today open-access in @Nature! Fantastic work @MireiaVallesc, the whole @cibiocm group @CIBIO_UniTrento and all the collaborators! https://t.co/EB4TFlIDIh
SaffronTree is bioinformatics software which allows you to take reads or contigs and quickly build a phylogenetic tree from them. It falls under the category of crazy ideas that turn out to be useful.
https://t.co/gtW5F0RLuG
I recently wondered: how well would @nanopore reads assemble in a short-read assembler? I.e. can ONT reads pass as Illumina reads in a de Bruijn graph assembly algorithm? Here are the results!
1/8
GitHub hosts more than 200.000.000 repositories.
But only a fraction of them are valuable resources for specific niches.
Here are 10 of my favorites repositories that help you grow as a software developer:
I have created pharokka, a dedicated fast phage annotation tool inspired by prokka. Pharokka is designed for users who want one-line, rapid, standarised and scalable phage annotations, much like prokka for prokaryotes. https://t.co/xIN2VClUeb
Bioinformatics post (2x available) at UKHSA in reference microbiology/bacterial genomics. just advertised. Please share to anyone who might be interested. https://t.co/O4KpN3SAOU
If you’re interested in making bioinformatics fast and scalable I’d hugely recommend this position with John who is one of the finest people I’ve been fortunate enough to work with.
@AvivaUK what is your policy about driving after local anaesthesia? That is topical injection of an anaesthetic in a localised area. Am I still insured to drive after the procedure?