@article{dd9f4b1455e34fb6b2a00b511f73cd15,
title = "Pandora: nucleotide-resolution bacterial pan-genomics with reference graphs",
abstract = "We present pandora, a novel pan-genome graph structure and algorithms for identifying variants across the full bacterial pan-genome. As much bacterial adaptability hinges on the accessory genome, methods which analyze SNPs in just the core genome have unsatisfactory limitations. Pandora approximates a sequenced genome as a recombinant of references, detects novel variation and pan-genotypes multiple samples. Using a reference graph of 578 Escherichia coli genomes, we compare 20 diverse isolates. Pandora recovers more rare SNPs than single-reference-based tools, is significantly better than picking the closest RefSeq reference, and provides a stable framework for analyzing diverse samples without reference bias.",
keywords = "Accessory genome, Genome graph, Nanopore, Pan-genome",
author = "Colquhoun, {Rachel M.} and Hall, {Michael B.} and Leandro Lima and Roberts, {Leah W.} and Malone, {Kerri M.} and Martin Hunt and Brice Letcher and Jane Hawkey and Sophie George and Louise Pankhurst and Zamin Iqbal",
note = "Funding Information: We are grateful to the REHAB consortium (https://modmedmicro.nsms.ox.ac.uk/rehab/) and the Transmission of Carbapenemase-producing Enterobacteriaceae (TRACE) study investigators for sharing sequencing data (for CFT073 and H131800734) in support of this work. We would like to thank Sion Bayliss and Ed Thorpe for discussions and help with Piggy. We are grateful to Kelly Wyres for sharing sequence data for the Australian samples, and to Tim Dallman and David Greig for sharing their data from Public Health England. We would like to thank the following for helpful conversations during the prolonged genesis of this project: Gil McVean, Derrick Crook, Eduardo Rocha, Bill Hanage, Ed Feil, Sion Bayliss, Ed Thorpe, Richard Neher, Camille Marchet, Rayan Chikhi, Kat Holt, Claire Gorrie, Rob Patro, Fatemeh Almodaresi, Nicole Stoesser, Liam Shaw, Phelim Bradley, and Sorina Maciuca. We would also like to thank the reviewers, with whose help the study was significantly improved. The review history is available as additional file 2. Andrew Cosgrove was the primary editor of this article and managed its editorial process and peer review in collaboration with the rest of the editorial team. Funding Information: RMC was funded by a Wellcome Trust PhD studentship (105279/Z/14/Z), and ZI was partially funded by a Wellcome Trust/Royal Society Sir Henry Dale Fellowship (102541/Z/13/Z). Open Access funding enabled and organized by Projekt DEAL. Publisher Copyright: {\textcopyright} 2021, The Author(s). Copyright: Copyright 2021 Elsevier B.V., All rights reserved.",
year = "2021",
month = dec,
doi = "10.1186/s13059-021-02473-1",
language = "English",
volume = "22",
journal = "Genome Biology",
issn = "1474-760X",
publisher = "BioMed Central",
number = "1",
}