@article{f1f84d6c9c8d4c328b1118fd6d3a1713,
title = "Optimizing sequencing protocols for leaderboard metagenomics by combining long and short reads",
abstract = "As metagenomic studies move to increasing numbers of samples, communities like the human gut may benefit more from the assembly of abundant microbes in many samples, rather than the exhaustive assembly of fewer samples. We term this approach leaderboard metagenome sequencing. To explore protocol optimization for leaderboard metagenomics in real samples, we introduce a benchmark of library prep and sequencing using internal references generated by synthetic long-read technology, allowing us to evaluate high-throughput library preparation methods against gold-standard reference genomes derived from the samples themselves. We introduce a low-cost protocol for high-throughput library preparation and sequencing.",
keywords = "Assembly, Benchmark, Binning, Leaderboard metagenome, Long reads",
author = "Sanders, {Jon G.} and Sergey Nurk and Salido, {Rodolfo A.} and Jeremiah Minich and Xu, {Zhenjiang Z.} and Qiyun Zhu and Cameron Martino and Marcus Fedarko and Arthur, {Timothy D.} and Feng Chen and Boland, {Brigid S.} and Humphrey, {Greg C.} and Caitriona Brennan and Karenina Sanders and James Gaffney and Kristen Jepsen and Mahdieh Khosroheidari and Cliff Green and Marlon Liyanage and Dang, {Jason W.} and Phelan, {Vanessa V.} and Quinn, {Robert A.} and Anton Bankevich and Chang, {John T.} and Rana, {Tariq M.} and Conrad, {Douglas J.} and Sandborn, {William J.} and Larry Smarr and Dorrestein, {Pieter C.} and Pevzner, {Pavel A.} and Rob Knight",
note = "Funding Information: This work was supported, in part, by an Illumina Medical Research Grant (LS and JTC), by Illumina support of the Center for Microbiome Innovation, and by funding from the NIH and the Alfred P. Sloan Foundation. CM was supported by a grant from the National Institutes of Health, USA (NIH grants T32GM8806). PAP was supported by NSF/MCB-BSF grant 1715911. SN and AB were supported by St. Petersburg State University grant 15.61.951.2015. TMR was supported by NIDA/NIH awards DA046171 and DA 039562. Publisher Copyright: {\textcopyright} 2019 The Author(s).",
year = "2019",
month = oct,
day = "31",
doi = "10.1186/s13059-019-1834-9",
language = "English (US)",
volume = "20",
pages = "1--14",
journal = "Genome biology",
issn = "1474-7596",
publisher = "BioMed Central",
number = "1",
}