Optimizing sequencing protocols for leaderboard metagenomics by combining long and short reads

Jon G. Sanders; Sergey Nurk; Rodolfo A. Salido; Jeremiah Minich; Zhenjiang Z. Xu; Qiyun Zhu; Cameron Martino; Marcus Fedarko; Timothy D. Arthur; Feng Chen; Brigid S. Boland; Greg C. Humphrey; Caitriona Brennan; Karenina Sanders; James Gaffney; Kristen Jepsen; Mahdieh Khosroheidari; Cliff Green; Marlon Liyanage; Jason W. Dang; Vanessa V. Phelan; Robert A. Quinn; Anton Bankevich; John T. Chang; Tariq M. Rana; Douglas J. Conrad; William J. Sandborn; Larry Smarr; Pieter C. Dorrestein; Pavel A. Pevzner; Rob Knight

doi:10.1186/s13059-019-1834-9

Optimizing sequencing protocols for leaderboard metagenomics by combining long and short reads

Jon G. Sanders, Sergey Nurk, Rodolfo A. Salido, Jeremiah Minich, Zhenjiang Z. Xu, Qiyun Zhu, Cameron Martino, Marcus Fedarko, Timothy D. Arthur, Feng Chen, Brigid S. Boland, Greg C. Humphrey, Caitriona Brennan, Karenina Sanders, James Gaffney, Kristen Jepsen, Mahdieh Khosroheidari, Cliff Green, Marlon Liyanage, Jason W. DangVanessa V. Phelan, Robert A. Quinn, Anton Bankevich, John T. Chang, Tariq M. Rana, Douglas J. Conrad, William J. Sandborn, Larry Smarr, Pieter C. Dorrestein, Pavel A. Pevzner, Rob Knight

Research output: Contribution to journal › Article › peer-review

35 Scopus citations

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.

Original language	English (US)
Article number	226
Pages (from-to)	1-14
Number of pages	14
Journal	Genome biology
Volume	20
Issue number	1
DOIs	https://doi.org/10.1186/s13059-019-1834-9
State	Published - Oct 31 2019
Externally published	Yes

Keywords

Assembly
Benchmark
Binning
Leaderboard metagenome
Long reads

ASJC Scopus subject areas

Ecology, Evolution, Behavior and Systematics
Genetics
Cell Biology

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10.1186/s13059-019-1834-9

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Sanders, J. G., Nurk, S., Salido, R. A., Minich, J., Xu, Z. Z., Zhu, Q., Martino, C., Fedarko, M., Arthur, T. D., Chen, F., Boland, B. S., Humphrey, G. C., Brennan, C., Sanders, K., Gaffney, J., Jepsen, K., Khosroheidari, M., Green, C., Liyanage, M., ... Knight, R. (2019). Optimizing sequencing protocols for leaderboard metagenomics by combining long and short reads. Genome biology, 20(1), 1-14. Article 226. https://doi.org/10.1186/s13059-019-1834-9

Sanders, JG, Nurk, S, Salido, RA, Minich, J, Xu, ZZ, Zhu, Q, Martino, C, Fedarko, M, Arthur, TD, Chen, F, Boland, BS, Humphrey, GC, Brennan, C, Sanders, K, Gaffney, J, Jepsen, K, Khosroheidari, M, Green, C, Liyanage, M, Dang, JW, Phelan, VV, Quinn, RA, Bankevich, A, Chang, JT, Rana, TM, Conrad, DJ, Sandborn, WJ, Smarr, L, Dorrestein, PC, Pevzner, PA & Knight, R 2019, 'Optimizing sequencing protocols for leaderboard metagenomics by combining long and short reads', Genome biology, vol. 20, no. 1, 226, pp. 1-14. https://doi.org/10.1186/s13059-019-1834-9

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AU - Salido, Rodolfo A.

AU - Minich, Jeremiah

AU - Xu, Zhenjiang Z.

AU - Zhu, Qiyun

AU - Martino, Cameron

AU - Fedarko, Marcus

AU - Arthur, Timothy D.

AU - Chen, Feng

AU - Boland, Brigid S.

AU - Humphrey, Greg C.

AU - Brennan, Caitriona

AU - Sanders, Karenina

AU - Gaffney, James

AU - Jepsen, Kristen

AU - Khosroheidari, Mahdieh

AU - Green, Cliff

AU - Liyanage, Marlon

AU - Dang, Jason W.

AU - Phelan, Vanessa V.

AU - Quinn, Robert A.

AU - Bankevich, Anton

AU - Chang, John T.

AU - Rana, Tariq M.

AU - Conrad, Douglas J.

AU - Sandborn, William J.

AU - Smarr, Larry

AU - Dorrestein, Pieter C.

AU - Pevzner, Pavel A.

AU - Knight, Rob

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Y1 - 2019/10/31

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AB - 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.

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KW - Benchmark

KW - Binning

KW - Leaderboard metagenome

KW - Long reads

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Optimizing sequencing protocols for leaderboard metagenomics by combining long and short reads

Abstract

Keywords

ASJC Scopus subject areas

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