Matches in SemOpenAlex for { <https://semopenalex.org/work/W2948252502> ?p ?o ?g. }
- W2948252502 abstract "Abstract Background Accurately identifying SNPs from bacterial sequencing data is an essential requirement for using genomics to track transmission and predict important phenotypes such as antimicrobial resistance. However, most previous performance evaluations of SNP calling have been restricted to eukaryotic (human) data. Additionally, bacterial SNP calling requires choosing an appropriate reference genome to align reads to, which, together with the bioinformatic pipeline, affects the accuracy and completeness of a set of SNP calls obtained. This study evaluates the performance of 41 SNP calling pipelines using simulated data from 254 strains of 10 clinically common bacteria and real data from environmentally-sourced and genomically diverse isolates within the genera Citrobacter, Enterobacter, Escherichia and Klebsiella . Results We evaluated the performance of 41 SNP calling pipelines, aligning reads to genomes of the same or a divergent strain. Irrespective of pipeline, a principal determinant of reliable SNP calling was reference genome selection. Across multiple taxa, there was a strong inverse relationship between pipeline sensitivity and precision, and the Mash distance (a proxy for average nucleotide divergence) between reads and reference genome. The effect was especially pronounced for diverse, recombinogenic, bacteria such as Escherichia coli , but less dominant for clonal species such as Mycobacterium tuberculosis . Conclusions The accuracy of SNP calling for a given species is compromised by increasing intra-species diversity. When reads were aligned to the same genome from which they were sequenced, among the highest performing pipelines was Novoalign/GATK. However, across the full range of (divergent) genomes, among the consistently highest-performing pipelines was Snippy." @default.
- W2948252502 created "2019-06-14" @default.
- W2948252502 creator A5001331694 @default.
- W2948252502 creator A5021299815 @default.
- W2948252502 creator A5026480684 @default.
- W2948252502 creator A5028335853 @default.
- W2948252502 creator A5030621715 @default.
- W2948252502 creator A5031551214 @default.
- W2948252502 creator A5055049959 @default.
- W2948252502 creator A5064800233 @default.
- W2948252502 creator A5071728473 @default.
- W2948252502 creator A5075264383 @default.
- W2948252502 date "2019-05-31" @default.
- W2948252502 modified "2023-09-27" @default.
- W2948252502 title "Genomic diversity affects the accuracy of bacterial SNP calling pipelines" @default.
- W2948252502 cites W1578830280 @default.
- W2948252502 cites W1579111454 @default.
- W2948252502 cites W1711571047 @default.
- W2948252502 cites W1882576502 @default.
- W2948252502 cites W1899170688 @default.
- W2948252502 cites W1964477845 @default.
- W2948252502 cites W1964807436 @default.
- W2948252502 cites W1966966274 @default.
- W2948252502 cites W1968828904 @default.
- W2948252502 cites W1978813754 @default.
- W2948252502 cites W1981394448 @default.
- W2948252502 cites W1982579644 @default.
- W2948252502 cites W1982855075 @default.
- W2948252502 cites W1984174967 @default.
- W2948252502 cites W1988282697 @default.
- W2948252502 cites W2007890464 @default.
- W2948252502 cites W2029657346 @default.
- W2948252502 cites W2033167804 @default.
- W2948252502 cites W2050109119 @default.
- W2948252502 cites W2060965924 @default.
- W2948252502 cites W2075429769 @default.
- W2948252502 cites W2076124986 @default.
- W2948252502 cites W2076359272 @default.
- W2948252502 cites W2083870688 @default.
- W2948252502 cites W2093931624 @default.
- W2948252502 cites W2094614987 @default.
- W2948252502 cites W2095763520 @default.
- W2948252502 cites W2096094352 @default.
- W2948252502 cites W2101793321 @default.
- W2948252502 cites W2103441770 @default.
- W2948252502 cites W2104240120 @default.
- W2948252502 cites W2108234281 @default.
- W2948252502 cites W2118442768 @default.
- W2948252502 cites W2119180969 @default.
- W2948252502 cites W2124465358 @default.
- W2948252502 cites W2125418992 @default.
- W2948252502 cites W2125840395 @default.
- W2948252502 cites W2133212095 @default.
- W2948252502 cites W2140067143 @default.
- W2948252502 cites W2146290346 @default.
- W2948252502 cites W2149753281 @default.
- W2948252502 cites W2153602357 @default.
- W2948252502 cites W2154468535 @default.
- W2948252502 cites W2158336776 @default.
- W2948252502 cites W2159954944 @default.
- W2948252502 cites W2161085554 @default.
- W2948252502 cites W2161815151 @default.
- W2948252502 cites W2168133698 @default.
- W2948252502 cites W2171203723 @default.
- W2948252502 cites W2173732482 @default.
- W2948252502 cites W2190569576 @default.
- W2948252502 cites W2236299009 @default.
- W2948252502 cites W2273187858 @default.
- W2948252502 cites W2311203695 @default.
- W2948252502 cites W2337747100 @default.
- W2948252502 cites W2341468196 @default.
- W2948252502 cites W2464112039 @default.
- W2948252502 cites W2467057731 @default.
- W2948252502 cites W2491124495 @default.
- W2948252502 cites W2509491391 @default.
- W2948252502 cites W2536199001 @default.
- W2948252502 cites W2586283250 @default.
- W2948252502 cites W2590415818 @default.
- W2948252502 cites W2596937542 @default.
- W2948252502 cites W2600407737 @default.
- W2948252502 cites W2605025138 @default.
- W2948252502 cites W2616026176 @default.
- W2948252502 cites W2727237484 @default.
- W2948252502 cites W2734764141 @default.
- W2948252502 cites W2774962890 @default.
- W2948252502 cites W2784788330 @default.
- W2948252502 cites W2789843538 @default.
- W2948252502 cites W2791837701 @default.
- W2948252502 cites W2893606925 @default.
- W2948252502 cites W2904213287 @default.
- W2948252502 cites W2911251965 @default.
- W2948252502 cites W2949149057 @default.
- W2948252502 cites W2950150251 @default.
- W2948252502 cites W2950354111 @default.
- W2948252502 cites W2951160681 @default.
- W2948252502 cites W2951176108 @default.
- W2948252502 cites W2951254987 @default.
- W2948252502 cites W2951529834 @default.
- W2948252502 cites W2952152744 @default.
- W2948252502 cites W2952167528 @default.