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Dorottya Nagy

@dotnagy.bsky.social

Bioinformatician, Infectious Disease Epidemiologist, Veterinary Surgeon

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Dorottya Nagy@dotnagy.bsky.social · 10mo ago

To summarise our recent pre-print: Autocycler, the automated consensus assembler, when used with Nanopore long-read only Enterobacterales assemblies, produces more complete chromosomes and plasmids, with an accuracy comparable to hybrid assemblies.

Figure 2 from my recently pre-printed manuscript on the completeness and accuracy of Nanopore long-read only bacterial genome assembly for Enterobacterales. a) tile plot of chromosome circularisation, with assembler on the x-axis and sample on the y-axis, shows that the consensus long-read only assembler, Autocycler, circularised more chromosomes at 95% (87/92) than any other long-read or hybrid assembler. b) complex upset plot of plasmid reconstruction, showing that the best plasmid reconstruction was achieved by long-read assemblers incorporating the separate plasmid assembly tool, Plassembler, namely Autocycler and Hybracter, reconstructing >96% of plasmids.
Dorottya Nagy@dotnagy.bsky.social · 10mo ago

Pleased to see this pre-printed, highlighting the completeness/accuracy of @nanoporetech.com long-read genome assembly for clinical Enterobacterales: www.biorxiv.org/content/10.1... Thanks to colleagues @modmedmicro.bsky.social, @ukhsa.bsky.social, @genewiz.bsky.social and @oxfordbrc.bsky.social!

Dorottya Nagy@dotnagy.bsky.social · 10mo ago

A highly inspiring week meeting fellow infectious disease researchers, and learning how to integrate genomics with infectious disease models! Feeling very fortunate to have been selected to attend this course. Thank you @training.ebi.embl.org for organising!

EMBL-EBI Training@training.ebi.embl.org · 11mo ago

Thank you to everyone who joined us this week for the @embo.org Practical Course 'Methods for infectious disease modelling using genomics'. Join us for 2026's EMBO Practical Course. Sign up for 'Causality in biomedicine' alerts and hear as this new course develops: www.ebi.ac.uk/training/eve... 🧬🧫