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 CC-BY-NC-ND 4.0 International license is made available under a The copyright holder for this preprint (which was not peer-reviewed) is the author/funder.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 ,000 reads in total, sequenced following capture with V ALL compared to pre-capture in 23 samples from the 2018 Lassa fever outbreak. Points are colored by the state in Nigeria that the sample is from (black is NTC). (b) Percent of LASV genome assembled, after use of V ALL , against the fraction of pre-capture reads that are LASV. Points to the left of the horizontal break correspond to samples with no LASV reads pre-capture. As in Fig. 4a , reads were downsampled to 200,000 before assembly. Points are colored as in (a). (c) Percent of LASV genome assembled, after use of V ALL . Here, reads were not downsampled before assembly. Bars are ordered as in Fig. 4a and colored by the state in Nigeria that the sample is from.