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Volume 26, Number 2—February 2020

Dispatch

Rapid Nanopore Whole-Genome Sequencing for Anthrax Emergency Preparedness

Heather P. McLaughlinComments to Author , Julia V. Bugrysheva, Andrew B. Conley, Christopher A. Gulvik, Blake Cherney, Cari B. Kolton, Chung K. Marston, Elke Saile, Erin Swaney, David Lonsway, Amy S. Gargis, Thiphasone Kongphet-Tran, Christine Lascols, Pierre Michel, Julie Villanueva, Alex R. Hoffmaster, Jay E. Gee, and David Sue
Author affiliations: Centers for Disease Control and Prevention, Atlanta, Georgia, USA (H.P. McLaughlin, J.V. Bugrysheva, C.A. Gulvik, B. Cherney, C.B. Kolton, C.K. Marston, E. Saile, D. Lonsway, A.S. Gargis, T. Kongphet-Tran, C. Lascols, P. Michel, J. Villanueva, A.R. Hoffmaster, J.E. Gee, D. Sue); IHRC–Georgia Tech Applied Bioinformatics Laboratory, Atlanta (A.B. Conley); Texas Department of State Health Services Laboratory, Austin, Texas, USA (E. Swaney)

Main Article

Table

De novo whole-genome assembly metrics for sequencing of Bacillus anthracis strain Ba0914*

Aligned to Mismatches Indels Contigs Nucleotide identity, %; average-fold coverage
Chromosome pXO1 pXO2
Ames reference strain
Nanopore 677 6,411 3 99.83; 54 99.78; 192 99.80; 91
SRS 526 180 35 99.96; 115 99.94; 467 99.94; 220
SRS assembly
Nanopore 166 6,305 NA 99.86 99.88 99.85

*Mismatches, indels, nucleotide identity, and average fold coverage for chromosomal and plasmid sequences of B. anthracis strain Ba0914 were determined on the basis of alignment with the Ames Ancestor reference strain assembly (top) or to the SRS-based Ba0914 strain assembly (bottom). The nanopore assembly was generated by using the first 120,000 live basecalled reads. Contigs, contiguous overlapping DNA segments; Indels, insertions and deletions; NA, not applicable; SRS, short-read sequencing.

Main Article

Page created: January 20, 2020
Page updated: January 20, 2020
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