期刊
GENOME BIOLOGY
卷 22, 期 1, 页码 -出版社
BMC
DOI: 10.1186/s13059-021-02473-1
关键词
Pan-genome; Genome graph; Accessory genome; Nanopore
资金
- Wellcome Trust [105279/Z/14/Z]
- Wellcome Trust/Royal Society Sir Henry Dale Fellowship [102541/Z/13/Z]
- Projekt DEAL
- Wellcome Trust [102541/Z/13/Z, 105279/Z/14/Z] Funding Source: Wellcome Trust
Pandora is a novel pan-genome graph structure and algorithm that can identify variants across the full bacterial pan-genome, providing a stable framework for analyzing diverse samples without reference bias.
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.
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