Supporting data for "Streaming algorithms for identification of pathogens and antibiotic resistance potential from real-time MinIONTM sequencing"
Dataset type: Genomic, Software
Data released on July 26, 2016
Cao MD; Ganesamoorthy D; Elliott AG; Zhang H; Cooper MA; Coin LJM (2016): Supporting data for "Streaming algorithms for identification of pathogens and antibiotic resistance potential from real-time MinIONTM sequencing" GigaScience Database. http://dx.doi.org/10.5524/100206
The recently introduced Oxford Nanopore MinION platform generates DNA sequence data in real-time. This has great potential to shorten the sample-to-results time and is likely to have bene ts such as rapid diagnosis of bacterial infection and identi cation of drug resistance. However, there are few tools available for streaming analysis of real-time sequencing data. Here, we present a framework for streaming analysis of MinION real-time sequence data, together with probabilistic streaming algorithms for species typing, strain typing and antibiotic resistance pro le identi cation. Using four culture isolate samples, as well as a mixed-species sample, we demonstrate that bacterial species and strain information can be obtained within 30 minutes of sequencing and using about 500 reads, initial drug-resistance pro les within two hours, and complete resistance pro les within 10 hours. While strain identi cation with multi-locus sequence typing required more than 15x coverage to generate con dent assignments, our novel gene-presence typing could detect the presence of a known strain with 0.5x coverage. We also show that our pipeline can process over 100 times more data than the current throughput of the MinION on a desktop computer.
Additional details
Read the peer-reviewed publication(s):
Additional information:
https://github.com/mdcao/npAnalysis
https://github.com/mdcao/japsa
Accessions (data generated as part of this study):
BioProject:
PRJEB14532
Sample ID | Taxonomic ID | Common Name | Genbank Name | Scientific Name | Sample Attributes |
---|---|---|---|---|---|
Klebsiella pneumoniae ATCC-13883 | 573 | Klebsiella pneumoniae | Isolation source:human urine Strain:ATCC-13883 Serovar:NCTC 9633, NCDC 298-53, NCDC 410-68 ... + | ||
Klebsiella pneumoniae ATCC-700603 | 1276653 | Klebsiella pneumoniae ATCC-700603 | Klebsiella pneumoniae ATCC-700603 | Isolation source:human urine Strain:ATCC-700603 Serovar:1000527, 7561 ... + | |
Klebsiella pneumoniae BAA-2146 | 1263871 | Klebsiella pneumoniae BAA-2146 | Klebsiella pneumoniae BAA-2146 | Isolation source:human urine Strain:ATCC BAA-2146 Serovar:K6, CCUG 45421, LMG 20218, MCV37 ... + |