Capturing diverse microbial sequence with comprehensive and scalable probe design

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

. CC-BY-NC-ND 4.0 International license is made available under a The copyright holder for this preprint (which was not peer-reviewed) is the author/funder. It . https://doi.org/10.1101/279570 doi: bioRxiv preprint There are n = 2 technical replicates for each choice of input copies, background amount, and use of capture (n = 1 replicate for the negative control with 0 copies). Each dot indicates percent of genome assembled, from 200,000 reads, in a replicate; line is through the mean of the replicates. Label to the right of each line indicates amount of background material. Assemblies are from read data presented in Fig. 3a. (b) Number of unique viral reads sequenced at increasing sequencing depth, from an input of 10 3 viral copies in different amounts of background. Horizontal axis gives the number of total reads to which a sample was subsampled. Each line is a technical replicate (n = 2) and shaded regions are 95% pointwise confidence bands calculated across random subsamplings. Dashed vertical line at 200,000 reads denotes the amount of total reads used in (a) and in Fig. 3a . Viral sequencing data generated after capture with V ALL saturates more quickly than without capture. (c) Same as (b), but from an input of 10 4 viral copies.