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Method

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

Method

Ultrasensitive allele inference from immune repertoire sequencing data with MiXCR

Artem Mikelov
George Nefediev
Alexander Tashkeev
Oscar L. Rodriguez
Diego Aguilar Ortmans
Valeriia Skatova Mark Izraelson Alexey N. Davydov Stanislav Poslavsky Souad Rahmouni
... [+5 authors] ...,
Corey T. Watson
Dmitriy Chudakov
Scott D. Boyd
Dmitry Bolotin

First Published October 21, 2024

Method

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

Method

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

Method

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

Method

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