Selected article for: "dilution series and EBOV genome"
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_86
    Snippet: To assess how the amount of viral content detected increases with sequencing depth (Supplementary Fig. 7b, c) , we used data from the Ebola dilution series on 10 3 and 10 4 copies. At these input amounts, both technical replicates, with and without capture and in both 30 ng and 300 ng of background, yielded at least 2 million sequencing reads. For each combination of input copies, background amount, technical replicate, and whether capture was us.....
    Document: To assess how the amount of viral content detected increases with sequencing depth (Supplementary Fig. 7b, c) , we used data from the Ebola dilution series on 10 3 and 10 4 copies. At these input amounts, both technical replicates, with and without capture and in both 30 ng and 300 ng of background, yielded at least 2 million sequencing reads. For each combination of input copies, background amount, technical replicate, and whether capture was used, we downsampled all raw reads to n = {1, 10, 100, 1000, 10000, 100000, 200000, 300000, . . . , 1900000, 2000000} reads. For each n, we performed this downsampling 5 times. We depleted reads with viral-ngs, aligned depleted reads to the EBOV reference genome (Supplementary Table 5 ), and counted the number aligned, as described above. We plotted the number of aligned reads for each subsampling amount in Supplementary Fig. 7b and c, where shaded regions are 95% pointwise confidence bands calculated across the 5 downsampling replicates.

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