Pandora: nucleotide-resolution bacterial pan-genomics with reference graphs

• Published in: Genome Biology Vol. 22; no. 1; p. 267
• Main Authors: Colquhoun, Rachel M, Hall, Michael B, Lima, Leandro, Roberts, Leah W, Malone, Kerri M, Hunt, Martin, Letcher, Brice, Hawkey, Jane, George, Sophie, Pankhurst, Louise, Iqbal, Zamin
• Format: Journal Article
• Language: English
• Published: England BioMed Central 14-09-2021; BMC
• Subjects: Accessory genome; Adaptability; Algorithms; Approximation; Bacteria; Bias; Escherichia coli - genetics; Genes; Genetic Variation; Genome graph; Genome, Bacterial; Genomes; Genomics; Genomics - methods; Genotype & phenotype; Genotypes; Graph representations; High-Throughput Nucleotide Sequencing; Method; Mutation; Nanopore; Nanopore Sequencing; Nucleotides; Pan-genome; Sequence Alignment; Sequence Analysis, DNA; Single-nucleotide polymorphism; Software; Nanopore; Accessory genome; Pan-genome; Genome graph
• ISSN: 1474-760X; 1474-7596; 1474-760X
• DOI: 10.1186/s13059-021-02473-1

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.