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Optimizing nanopore adaptive sampling for pneumococcal serotype surveillance in complex samples using the graph-based GNASTy algorithm

  • Samuel T. Horsfield
  • Basil C.T. Fok
  • Yuhan Fu
  • Paul Turner
  • John A. Lees
  • Nicholas J. Croucher
  • First Published March 4, 2025

k-mer analysis" > Seamless, rapid, and accurate analyses of outbreak genomic data using split k-mer analysis

  • Romain Derelle
  • Johanna von Wachsmann
  • Tommi Mäklin
  • Joel Hellewell
  • Timothy Russell
  • Ajit Lalvani
  • ... [+1 authors] ...,
  • Leonid Chindelevitch
  • Nicholas J. Croucher
  • Simon R. Harris
  • John A. Lees
  • First Published October 15, 2024

Pangenome-spanning epistasis and coselection analysis via de Bruijn graphs

  • Juri Kuronen
  • Samuel T. Horsfield
  • Anna K. Pöntinen
  • Sudaraka Mallawaarachchi
  • Sergio Arredondo-Alonso
  • Harry Thorpe Rebecca A. Gladstone Rob J.L. Willems Stephen D. Bentley Nicholas J. Croucher
  • ... [+5 authors] ...,
  • Johan Pensar
  • John A. Lees
  • Gerry Tonkin-Hill
  • Jukka Corander
  • First Published August 12, 2024

Accurate and fast graph-based pangenome annotation and clustering with ggCaller

  • Samuel T. Horsfield
  • Gerry Tonkin-Hill
  • Nicholas J. Croucher
  • John A. Lees
  • First Published August 24, 2023

Fast and flexible bacterial genomic epidemiology with PopPUNK

  • John A. Lees
  • Simon R. Harris
  • Gerry Tonkin-Hill
  • Rebecca A. Gladstone
  • Stephanie W. Lo
  • Jeffrey N. Weiser
  • Jukka Corander
  • Stephen D. Bentley
  • Nicholas J. Croucher
  • First Published January 24, 2019
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