Got milk virus genomes? (or any H5N1?) Throw them at https://t.co/Carfmuc0N1 and see where they land in per-segment trees of tens of thousands of public Influenza A H5N1 sequences!
My colleagues and I have just posted a
"Note about availability of #H5N1 2.3.4.4b consensus sequences from cattle and other species" @virological_org.
Consensus genomes and metadata.
https://t.co/ggfgW4FPYa
#GPUalgorithms achieve significant speedup in statistical #phylogenetics, exemplified by estimating West Nile virus introduction timing from 104 genomes using BEAGLE v4.0.0 in BEAST. [co-authored by EVBC members @LemeyLab@suchard_group] https://t.co/sa5ACZfaSW
We've been working hard to enable quicker and easier ⚡️ access to simple but key SC2 variant statistics 📉📈 on @DiseaseOutbreak
Our R package now lets any user with @GISAID credentials to quickly access these stats for surveillance efforts 🔍 & complex downstream analyses 🤓
In a @VanityFair story, @KatherineEban oddly misrepresented an investigation into @GISAID and Peter Bogner by @sciencecohen and me; suggested our story was a volley in the lab leak debate; and let Bogner dismiss it as a "hit piece." Here's our response. https://t.co/v8FMgeHz2L
My colleague @sciencecohen and I spent months investigating @GISAID and the mysterious man behind it, Peter Bogner. Here's what we found. https://t.co/FVfswDnAD5
Had a good week participating in the NCBI Beyond Phylogenies codeathon. One of the things our team achieved was to add links between tools used for viral phylogenetics
You can now:
- load @nextstrain trees in Taxonium
- export out NS subtrees
- get clade stats with @GenSpectrum
🧵for our latest preprint on the intrahost evolution of SARS-CoV-2 virus in an immunocompromised individual (60s) with a history of cancer chronically infected for at least 471 days (ongoing) with consistently replicating viruses at a high viral load. 1/n
https://t.co/qBNEjXTqMt
@TWenseleers @RobLanfear @flaneuseks @K_G_Andersen I’m not aware of such an R package but might be worth connecting with GISAID regarding their api feeds through which they provide programmatic access.
@TWenseleers @RobLanfear @flaneuseks @K_G_Andersen Sorry but the API can only be used to access the aggregated metrics on our database. The direct downloads are accessible only via GISAID.
@flaneuseks @RobLanfear @K_G_Andersen In the meantime, we actually have this endpoint that can be access in a hacky way thru R pkg.
url <- "https://t.co/1pLMFwgI2C"
df <- getGenomicsResponse(url)[[1]]
This was a big team effort only made possible by global 🗺️ sequencing efforts and the team at @GISAID!
In particular, I wanted to highlight @malkuzweny's work in building the R package. She has gone on to doing more exciting work as a PhD student in @TAlexPerkins's group!
We've also described the technical details on https://t.co/33nZjrFuEy in these preprints,
Genomic reports
https://t.co/R1OfknTYHy
Research Library
https://t.co/n0092l4YKw