james hadfield

Phylogeneticist. Work for @trvrb & @nextstrain. Behind RAMPART (@NetworkArtic) & Phandango. PhD Cambridge. New Zealand is home.

[james hadfield @hamesjadfield]

@BillHanage Completely upside down. But that's because I'm now back in New Zealand ;)

[james hadfield @hamesjadfield]

@ogrecio @NetworkArtic regarding accessing rampart using a given IP, I _think_ you're wanting a reverse proxy or something more temporary like https://t.co/d5qIfpKK1v (aside: you can easily change the ports, see `rampart --help`). 2/2

[james hadfield @hamesjadfield]

@ogrecio @NetworkArtic Hi Oscar -- for the protocol, see https://t.co/0J95cFgxYM 1/2

[james hadfield @hamesjadfield]

@BillHanage All good points Bill. In terms of the stats used in the paper I found Andrew Gelman's run-through really helpful https://t.co/DE8ZjLEaf7

[james hadfield @hamesjadfield]

@GageKMoreno @nextstrain @KATarinambraun @dho_lab @tcfriedrich Congrats on getting this local build set up & running auspice yourself 💯. Let us know if you're interested in having your own nextstrain group (e.g. https://t.co/aDpDmlkLVq) which you could upload datasets & narratives to

[james hadfield @hamesjadfield]

@arambaut @nextstrain Frustrating & unsurprising. Hopefully when all is said and done the insights made possible by data sharing, virological, nextstrain etc will be seen as the way forward.

[james hadfield @hamesjadfield]

@B_Gutierrez_G @firefoxx66 @nextstrain @richardneher @trvrb Yeah this is a great example Bernado (and to think how many analogous situations exist due to incomplete sampling!). We're working on improving this, esp for singletons/cherries etc as Emma said. Ideas welcome from the ox crew BTW!

[james hadfield @hamesjadfield]

@mattloose @bioinfomatt @nanopore @scastesparraka @samstudio8 rampart is becoming a bit rampant, but in a good way I hope 😉

[james hadfield @hamesjadfield]

@Psy_Fer_ @NetworkArtic Yes 🎉 but read this first re double barcoding: https://t.co/aUFpPipjZQ. We'll try to get the artic-ncov2019 env updated too.

[james hadfield @hamesjadfield]

. @NetworkArtic RAMPART v1.1.0 released, w support for guppy-demuxed fastqs, fixes out-of-memory bugs + bunch of other improvements. More frequent releases on the way 🤞. More details: https://t.co/20QBXNFOlx

It's been great to see this being used -- keep up the good work!

[Deep Seq @DeepSeqNotts]

12 covid-19 samples on to contribute to the work of the COG-UK consortium. Thanks to team and all at @UoNLifeSci @UniofNottingham #WeareUoN

[Gage Moreno @GageKMoreno]

@NetworkArtic V3 #SARSCoV2 / #HCoV19 primers on 15 samples. 5 minutes in. I’d say it’s a success! @nanopore @KATarinambraun

[Eric Topol @EricTopol]

The #genomics of #COVID19 from the scientists who 1st sequenced it, its origin, and how it relates to the previous coronavirus epidemics
https://t.co/1MhPL0FSY8 @CellPressNews @CellCellPress

[james hadfield @hamesjadfield]

65 genomes added to @nextstrain (https://t.co/wb1AwuBMzw) **today**

[james hadfield @hamesjadfield]

@nextstrain @ESRNewZealand @MathStorey @Joepdl @sciolato @MathStorey @Joepdl was the NZ genome (20VR0206) an independent travel history to Iran, or linked to NZ01?

[james hadfield @hamesjadfield]

@klevy_emory @nextstrain Hey Karen, these are still accessible but we haven't got a list of URLs up. If you load the current sit-rep (https://t.co/Qjtrh41Ijl) then change the date ("2020-03-20") in the URL to "2020-01-23", "2020-01-25", "2020-01-30", "2020-03-04", "2020-03-05", "2020-03-13"

[james hadfield @hamesjadfield]

@Joepdl @phydyn @hendysh @Bureauchem @nextstrain Doing a great job Joep, Matt, Una et al. Is there a (public) way to link https://t.co/49ZXwNvK9H to the genome names (20VR0189, 20VR019 etc).

[james hadfield @hamesjadfield]

Sunday's update 👇

The fact we are picking up so many cases is a credit to NZ testing capacity, with ~6k tests done now (still working on incorporating test numbers & rate of +ves here)

[james hadfield @hamesjadfield]

Update: now 28 NZ cases, all linked to overseas travel. (Cases now scaled to pop size.)

Priority is avoiding community spread & widespread testing will be crucial for this. More testing=more knowledge. We're in a relatively strong position at this stage but we have to act fast.

[james hadfield @hamesjadfield]

Today's update: 11 +ve out of ~1000 tests. Amazing job to get this much testing capacity. I'll try to get those data to plot in the coming days, that's the success story here.