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Andrew Page @andrewjpage@mstdn.science Profile picture
@andrewjpage
Jun 1, 2020 • 4 tweets • 3 min read • Read on X
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.
One issue I did find was that theres very little #nanopore data for Mtb, which is disappointing since its such an important pathogen (@danybeste & Suzie Hingley-Wilson set me straight on that one)
Fingers crossed someone like @ZaminIqbal will announce they've a secret set of 100k Mtb samples sequenced on #nanopore so that galru can get a good workout...

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More from @andrewjpage

Andrew Page @andrewjpage@mstdn.science Profile picture
Oct 1, 2020
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.
Interestingly we found 16 lineages in healthcare workers (& families) which were not observed in patients or in community care. This indicates infection control measures were working.
Read 10 tweets
Andrew Page @andrewjpage@mstdn.science Profile picture
Aug 13, 2020
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.
Paper: preprints.org/manuscript/202…
Specification technical documents: github.com/pha4ge/SARS-Co……-Data-Specification
Protocols for submitting to all the archives: protocols.io/workspaces/pha…
Read 4 tweets
Andrew Page @andrewjpage@mstdn.science Profile picture
Jun 25, 2020
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.
We sequenced the same subset of SARS-CoV-2 samples using #Illumina, standard #Nanopore with ligation, and CoronaHiT (48 and 94 samples) with a range of Cts. All raw data in ENA, so useful on its own for comparisons, thanks to @happy_khan
Read 4 tweets
Andrew Page @andrewjpage@mstdn.science Profile picture
May 22, 2020
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.
11 local lineages are still bubbling away and fingers crossed the next batch of 380 samples being sequenced today, collected over the last 1.5 weeks, will bring more good news.
Read 4 tweets
Andrew Page @andrewjpage@mstdn.science Profile picture
May 14, 2020
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.
Teams at @NNUH Cotman Centre & Cytology work round the clock to test for SARS-CoV-2.Another team prepares the samples & brings them to @TheQuadram, another team prepares the RNA using the @NetworkArtic protocol, another team makes the libraries & sequences.
Read 5 tweets

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