Selected article for: "genome detection and metagenomic sequencing"
Author: Hayden C. Metsky; Katherine J. Siddle; Adrianne Gladden-Young; James Qu; David K. Yang; Patrick Brehio; Andrew Goldfarb; Anne Piantadosi; Shirlee Wohl; Amber Carter; Aaron E. Lin; Kayla G. Barnes; Damien C. Tully; Björn Corleis; Scott Hennigan; Giselle Barbosa-Lima; Yasmine R. Vieira; Lauren M. Paul; Amanda L. Tan; Kimberly F. Garcia; Leda A. Parham; Ikponmwonsa Odia; Philomena Eromon; Onikepe A. Folarin; Augustine Goba; Etienne Simon-Lorière; Lisa Hensley; Angel Balmaseda; Eva Harris; Douglas Kwon; Todd M. Allen; Jonathan A. Runstadler; Sandra Smole; Fernando A. Bozza; Thiago M. L. Souza; Sharon Isern; Scott F. Michael; Ivette Lorenzana; Lee Gehrke; Irene Bosch; Gregory Ebel; Donald Grant; Christian Happi; Daniel J. Park; Andreas Gnirke; Pardis C. Sabeti; Christian B. Matranga
Title: Capturing diverse microbial sequence with comprehensive and scalable probe design
  • Document date: 2018_3_12
    • ID: a9lkhayg_28
    Snippet: We selected 23 samples, spanning 5 states in Nigeria, that yielded either no portion of a LASV genome or only partial genomes with unbiased metagenomic sequencing even at high sequencing depth (> 4.5 million reads) 49 , and performed capture on these using V ALL . At equivalent pre-and post-capture sequencing depth (200,000 reads), use of V ALL improved our ability to detect and assemble LASV. Capture considerably increased the amount of unique L.....
    Document: We selected 23 samples, spanning 5 states in Nigeria, that yielded either no portion of a LASV genome or only partial genomes with unbiased metagenomic sequencing even at high sequencing depth (> 4.5 million reads) 49 , and performed capture on these using V ALL . At equivalent pre-and post-capture sequencing depth (200,000 reads), use of V ALL improved our ability to detect and assemble LASV. Capture considerably increased the amount of unique LASV material detected in all 23 samples (in 4 samples, by more than 100×), and in 7 samples it enabled detection when there were no LASV reads pre-capture ( Supplementary Fig. 10a , Supplementary Table 7) . This in turn improved genome assembly. Whereas precapture we could not assemble any portion of a genome in 22 samples (in the remaining one, 2% of a genome) at this depth, following use of V ALL we could assemble a partial genome in 22 of the 23 (Fig. 4a, Supplementary Fig. 10b ); most were small portions of a genome, although in 7 we assembled > 50% of a genome. Assembly results with V ALL are comparable without downsampling ( Supplementary Fig. 10c ), likely because we saturate unique content with V ALL even at low sequencing depths ( Supplementary Fig. 7b , c). These results illustrate how V ALL can be used to improve viral detection and genome assembly in an outbreak, especially at the low sequencing depths that may be desired or required in these settings.

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