| Title: |
Pandora: nucleotide-resolution bacterial pan-genomics with reference graphs |
| Authors: |
Rachel M. Colquhoun, Michael B. Hall, Leandro Lima, Leah W. Roberts, Kerri M. Malone, Martin Hunt, Brice Letcher, Jane Hawkey, Sophie George, Louise Pankhurst, Zamin Iqbal |
| Source: |
Genome Biology, Vol 22, Iss 1, Pp 1-30 (2021) |
| Publisher Information: |
BMC, 2021. |
| Publication Year: |
2021 |
| Collection: |
LCC:Biology (General)
LCC:Genetics |
| Subject Terms: |
Pan-genome, Genome graph, Accessory genome, Nanopore, Biology (General), QH301-705.5, Genetics, QH426-470 |
| More Details: |
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. |
| Document Type: |
article |
| File Description: |
electronic resource |
| Language: |
English |
| ISSN: |
1474-760X |
| Relation: |
https://doaj.org/toc/1474-760X |
| DOI: |
10.1186/s13059-021-02473-1 |
| Access URL: |
https://doaj.org/article/3bf384fd17904ec49e3cda3805c804b4 |
| Accession Number: |
edsdoj.3bf384fd17904ec49e3cda3805c804b4 |
| Database: |
Directory of Open Access Journals |
