Pandora: nucleotide-resolution bacterial pan-genomics with reference graphs
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...
| Principais autores: | , , , , , , , , , , |
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| Formato: | Journal article |
| Idioma: | English |
| Publicado em: |
BioMed Central
2021
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| _version_ | 1826307863362928640 |
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| author | Colquhoun, RM Hall, MB Lima, L Roberts, LW Malone, KM Hunt, M Letcher, B Hawkey, J George, S Pankhurst, L Iqbal, Z |
| author_facet | Colquhoun, RM Hall, MB Lima, L Roberts, LW Malone, KM Hunt, M Letcher, B Hawkey, J George, S Pankhurst, L Iqbal, Z |
| author_sort | Colquhoun, RM |
| collection | OXFORD |
| description | 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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| first_indexed | 2024-03-07T07:09:24Z |
| format | Journal article |
| id | oxford-uuid:8f804b71-cd05-4eeb-8ba3-ab17d08a7b79 |
| institution | University of Oxford |
| language | English |
| last_indexed | 2024-03-07T07:09:24Z |
| publishDate | 2021 |
| publisher | BioMed Central |
| record_format | dspace |
| spelling | oxford-uuid:8f804b71-cd05-4eeb-8ba3-ab17d08a7b792022-06-14T06:46:31ZPandora: nucleotide-resolution bacterial pan-genomics with reference graphsJournal articlehttp://purl.org/coar/resource_type/c_dcae04bcuuid:8f804b71-cd05-4eeb-8ba3-ab17d08a7b79EnglishSymplectic ElementsBioMed Central2021Colquhoun, RMHall, MBLima, LRoberts, LWMalone, KMHunt, MLetcher, BHawkey, JGeorge, SPankhurst, LIqbal, ZWe 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. |
| spellingShingle | Colquhoun, RM Hall, MB Lima, L Roberts, LW Malone, KM Hunt, M Letcher, B Hawkey, J George, S Pankhurst, L Iqbal, Z Pandora: nucleotide-resolution bacterial pan-genomics with reference graphs |
| title | Pandora: nucleotide-resolution bacterial pan-genomics with reference graphs |
| title_full | Pandora: nucleotide-resolution bacterial pan-genomics with reference graphs |
| title_fullStr | Pandora: nucleotide-resolution bacterial pan-genomics with reference graphs |
| title_full_unstemmed | Pandora: nucleotide-resolution bacterial pan-genomics with reference graphs |
| title_short | Pandora: nucleotide-resolution bacterial pan-genomics with reference graphs |
| title_sort | pandora nucleotide resolution bacterial pan genomics with reference graphs |
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