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Predicting antibiotic resistance de novo

New preprint: processing 3.9 million SARS-CoV-2 samples to make a consistent phylogenetic tree

Philip Fowler, 7th May 20247th May 2024

Martin Hunt, Zam Iqbal and lots of others have written an epic preprint where they describe their variant caller, viridian, that was written expressly for producing a consensus genome for a virus using tiled amplicon sequencing. We deployed viridian into our cloud-based sequencing platform during the pandemic and several of us are co-authors on the preprint.

Rather than just write a straightforward methods paper, they choose to take it a few steps further and download all the publicly available SARS-CoV-2 FASTQ files from the ENA (which was about 3.9 million) and process them with viridian and then build a phylogenetic tree that is missing some of the artefacts that plague the trees if you simply take FASTA files that have been deposited using a range of genetic pipelines.

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