Journal article
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.
- Publication status:
- Published
- Peer review status:
- Peer reviewed
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- Files:
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(Preview, Version of record, 1.9MB, Terms of use)
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- Publisher copy:
- 10.1186/s13059-021-02473-1
Authors
- Publisher:
- BioMed Central
- Journal:
- Genome Biology More from this journal
- Volume:
- 22
- Article number:
- 267
- Publication date:
- 2021-09-14
- Acceptance date:
- 2021-08-19
- DOI:
- EISSN:
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1474-760X
- ISSN:
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1474-7596
- Pmid:
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34521456
- Language:
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English
- Keywords:
- Pubs id:
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1195799
- Local pid:
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pubs:1195799
- Deposit date:
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2022-06-13
Terms of use
- Copyright holder:
- Colquhoun et al.
- Copyright date:
- 2021
- Rights statement:
- Copyright © 2021 The Author(s). This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
- Licence:
- CC Attribution (CC BY)
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