Dear UCSC genomics, thank you very much for making available the web version of UShER (https://genome.ucsc.edu/cgi-bin/hgPhyloPlace). I use it to assign lineages of SARS-CoV-2 to those which are “unassigned” by other methods (e.g. Pangolin, Scorpio). I use the sequence ID’s as the input file
I have one question – is there an upper limit to the number of ID’s that can be submitted in one form? At present I see it can take a few hundred, but not thousands. Presumably there is some cut-off as to the number of ID’s/sequences that it can handle.
Best wishes
Mike Elmore
Dr Mike Elmore
Bioinformatician
UK Health Security Agency
Porton Down
Salisbury
Wiltshire
SP4 0JG
Follow us on twitter @UKHSA
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Dear, Luis, thank you for your reply and the explanation. I work at one step removed from the actual program, in that I interrogate COG-UK Covid Metadata files (https://www.cogconsortium.uk/priority-areas/data-linkage-analysis/public-data-analysis/), which have already had their lineages called. The limited lineage information states “PLEARN-v1.14”, which I assume tallies with “Pangolin-data” version on the Pangolin website, but it doesn’t state the Pango program version.
I’ll see if we can get the standalone version up and running at my establishment
Thank you for your help and explanation
Best Wishes
Mike Elmore
From: Luis Nassar <lrna...@ucsc.edu>
Sent: 10 September 2022 01:06
To: Mike Elmore <Mike....@ukhsa.gov.uk>
Cc: gen...@soe.ucsc.edu
Subject: Re: [genome] UShER: Ultrafast Sample placement on Existing tRee - is there a limit to the number of ID's that can be processed via the web browser version?
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