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_24
Snippet: Quantifying within-sample diversity after capture: co-infections and within-host nucleotide variants Identity between probe and assembled H4N4 sequence (%) 40 60 80 100 log 2 (fold-change in depth) Relation between probe-target identity and enrichment in read depth, as seen after capture with V ALL and with V WAFR on an Influenza A virus sample of subtype H4N4 (IAV-SM5). Each point represents a window in the IAV genome. Identity between the probe.....
Document: Quantifying within-sample diversity after capture: co-infections and within-host nucleotide variants Identity between probe and assembled H4N4 sequence (%) 40 60 80 100 log 2 (fold-change in depth) Relation between probe-target identity and enrichment in read depth, as seen after capture with V ALL and with V WAFR on an Influenza A virus sample of subtype H4N4 (IAV-SM5). Each point represents a window in the IAV genome. Identity between the probe and assembled H4N4 sequence is a measure of identity between the sequence in that window and the top 25% of probe sequences that map to it (see Methods for details). Fold-change in depth is averaged over the window. No sequences of segment 6 (N) of the N4 subtypes were included in the design of V ALL or V WAFR . (c) Effect of capture on estimated frequency of within-sample co-infections. RNA of 2, 4, 6, and 8 viral species were spiked into extracted RNA from healthy human plasma and then captured with V ALL and V WAFR . Values on top are the percent of all sequenced reads that are viral. We did not detect Nipah virus (NiV) using the V WAFR probe set because this virus was not present in that design. (d) Effect of capture on estimated frequency of within-host variants, shown in positions across three dengue virus samples: DENV-SM1, DENV-SM2, and DENV-SM5. Capture with V ALL and V WAFR was each performed on n = 2 replicates of the same library. Ïc indicates concordance correlation coefficient between pre-and post-capture frequencies.
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