Rachel Colquhoun

Postdoc at Edinburgh Uni in Rambaut lab. Work: @nanopore for viruses and gram-neg bacteria, population reference graphs, metagenomes @[email protected]

[Rachel Colquhoun @rmcolq]

Very excited to see our paper on using reference graphs to allow genotyping of both core AND ACCESSORY variation in bacteria https://t.co/xJGfyMPCiJ. This is the culmination of a huge amount of work by @mbhall88 @leandro_ishi @ZaminIqbal and more

[Russ Corbett @RussCorbett]

Pango lineages (e.g., B.1.1.7 “alpha”) are the lingua franca of genomic epidemiology and an awesome example of open science. Maintaining Pango is also a ton of work! In our latest preprint @jdm1771 addresses this with autolin, a method for automated lineage proposals.

[Rachel Colquhoun @rmcolq]

@user3425664 No lineages have been deleted, just not all are displayed on that page

[Rachel Colquhoun @rmcolq]

@AineToole @OrlaDV @tcdgenmicro That gown is amazing!

[Rachel Colquhoun @rmcolq]

@gsgs2 There is a 1-1 mapping between the trimmed alignment and metadata tables. Dropouts are filtered almost always either because their sequence quality is low or as duplicates

[Rachel Colquhoun @rmcolq]

@samstudio8 Sadly I have

[Rachel Colquhoun @rmcolq]

@joel_mossong @arambaut @PangoNetwork It's frustrating that it changes, but it shouldn't change historic cluster investigations. You can't have a system specifically to label small differences in an evolving virus which could be epidemiologically relevant without updating nomenclature in real time

[Rachel Colquhoun @rmcolq]

@joel_mossong @arambaut @PangoNetwork You don't have to use it. It's a tool to do a job (describing virus genetic diversity as it evolves in real time). Bacterial sequence typing methods have their own problems and solve a completely different question

[Rachel Colquhoun @rmcolq]

@DannyJPark @arambaut @PangoNetwork No - scorpio is the tool, and https://t.co/BQMYU8pgF9 is the data repo. There was a new constellations release earlier today. Running pangolin --update should make sure the new lineage is called by pangolin

[Rachel Colquhoun @rmcolq]

This checks that a sequence meets the definition of an AY.4 lineage classification and additionally has 3 of the following mutations: spike:Y145H, spike:A222V, nuc:T17040C, nuc:C25614T.

[Rachel Colquhoun @rmcolq]

New pangoLEARN model now available for @PangoNetwork designation version v1.2.86 that can assign newly designated lineage AY.4.2. :loudspeaker: https://t.co/T08HJWDPAd

[Rachel Colquhoun @rmcolq]

Given the interest in AY.4.2 and known issues with @NetworkArtic V3 primer dropout over the spike:Y145H mutation, pangolin uses scorpio to sanity-check AY.4.2 lineage assignments.

[Rachel Colquhoun @rmcolq]

@Amandatron89 @Jammyllama @UnicornMarCo @ION_BRU Does it work with mixed sequence data e.g. different versions of same virus?

[Rachel Colquhoun @rmcolq]

@ZaminIqbal Are they better or worse than the caramel ones? Depending on answer, may have to find a shop tomorrow

[Rachel Colquhoun @rmcolq]

@CorneliusRoemer @JosetteSchoenma @DiseaseOutbreak Also, it doesn't make a lot of different if https://t.co/z6mipIP4nk include lineages which have been designated but not released in their list. We normally designate and release in one go (this is an exception), and pango-designations lag behind model training for pangolin anyway

[Rachel Colquhoun @rmcolq]

@CorneliusRoemer @JosetteSchoenma @DiseaseOutbreak There was some internal discussion within the designation committee about the proposed AY.33 and AY.33.1. These lineages will be released when the set of representative sequences has been decided for AY.33.

[Rachel Colquhoun @rmcolq]

@KarelBrinda @RayanChikhi @mbhall88 @leandro_ishi @ZaminIqbal Thanks Karel!

[Rachel Colquhoun @rmcolq]

Very excited to see our paper on using reference graphs to allow genotyping of both core AND ACCESSORY variation in bacteria https://t.co/xJGfyMPCiJ. This is the culmination of a huge amount of work by @mbhall88 @leandro_ishi @ZaminIqbal and more

[Rachel Colquhoun @rmcolq]

Since the preprint, there have also been big performance and usability improvements thanks to both @mbhall88 and @leandro_ishi.

[Rachel Colquhoun @rmcolq]

There's lots of neat stuff under the hood, including building graphs from MSA avoiding blowups, indexing graphs with minimizers, quasi-mapping instead of alignment, de novo discovery of new variants @mbhall88, rapid PanRG updates using a memorised recursion tree @leandro_ishi.