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Andrew Page @andrewjpage@mstdn.science Profile picture
Andrew Page @andrewjpage@mstdn.science
@andrewjpage
Director of Technical Innovation @theiagen, co-host MicroBinfie Podcast, develop tools for microbial bioinformatics & a runner
Oct 1, 2020 • 10 tweets • 4 min read
We sequenced 1500 people with Coronavirus in #Norfolk over the 1st wave & have a paper out today with lots of interesting findings: medrxiv.org/content/10.110… We found 100 different lineages in circulation in Norfolk, a region of about 1 million people.
Aug 13, 2020 • 4 tweets • 3 min read
The MicroBinfie podcast talks to @dmaccannell @DoctorRuth @griffiemma about the @pha4ge SARS-CoV-2 contextual data specification for open genomic epidemiology in this episode
Spotify: open.spotify.com/episode/0X6kx3…
iTunes: podcasts.apple.com/gb/podcast/26-…
SoundCloud: soundcloud.com/microbinfie/26… They have brought together a global consortium of scientists who are sequencing #SARSCoV2 to help make the metadata interoperable and as useful as possible.
Jun 25, 2020 • 4 tweets • 4 min read
Our new method for multiplexing 94 SARS-CoV-2 samples on a #Nanopore #MinION flowcell for £12.72 per sample (extracted RNA to sequencing) biorxiv.org/content/10.110… It's a simplified lab protocol, which is faster and cheaper, utilising Nextera. We combined it with 96 #Nanopore PCR barcodes, so guppy deplexes out of the box.
Jun 1, 2020 • 4 tweets • 3 min read
Galru is out today. Its for spoligotyping Mycobacterium #tuberculosis directly from #Nanopore data, and you can get a type from as little as a single read.
Paper: biorxiv.org/cgi/content/sh…
Software: github.com/quadram-instit…
Install: conda install galru Its a combined effort with @happy_khan @thanhleviet @timskvortsov Michael Strinden. Galrú is Irish (Gaeilge) for infection in keeping with my recent naming scheme.
May 22, 2020 • 4 tweets • 2 min read
A 1st look at the #SARSCoV2 genomes we've sequenced at @TheQuadram shows 116 local lineages. Most of these local lineages only have 1 sample. 14 lineages have more than 5 samples & there is a strong geographic signal for lineages (local transmission). The good news is that 3 of these big local lineages appear to have been stopped in their tracks and haven't been seen in weeks! The fact that we can see this rapidly in the data is amazing. It shows us that measures are working.
May 14, 2020 • 5 tweets • 3 min read
Another 380 SARS-CoV-2 genomes from Norfolk and Suffolk just about to roll off the sequenced at @TheQuadram for @CovidGenomicsUK Image We work in plates of 96 samples (95 SARS-CoV-2+1 control). This week 4 plates were sequenced on a high output #Illumina NextSeq500. Over a dozen clinicians in @NNUH and scientists in @TheQuadram worked long hours to make this happen.