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

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

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 opt...

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Published in:Genome Biology Vol. 20; no. 1; p. 226
Main Authors: Sanders, Jon G, Nurk, Sergey, Salido, Rodolfo A, Minich, Jeremiah, Xu, Zhenjiang Z, Zhu, Qiyun, Martino, Cameron, Fedarko, Marcus, Arthur, Timothy D, Chen, Feng, Boland, Brigid S, Humphrey, Greg C, Brennan, Caitriona, Sanders, Karenina, Gaffney, James, Jepsen, Kristen, Khosroheidari, Mahdieh, Green, Cliff, Liyanage, Marlon, Dang, Jason W, Phelan, Vanessa V, Quinn, Robert A, Bankevich, Anton, Chang, John T, Rana, Tariq M, Conrad, Douglas J, Sandborn, William J, Smarr, Larry, Dorrestein, Pieter C, Pevzner, Pavel A, Knight, Rob
Format: Journal Article
Language:English
Published: England BioMed Central 31-10-2019
BMC
Subjects:
Animals
Assembly
Benchmark
Benchmarking
Binning
Gastrointestinal Microbiome
Genomic Library
High-Throughput Nucleotide Sequencing
Humans
Leaderboard metagenome
Long reads
Metagenomics - methods
Method
Mice
Benchmark
Leaderboard metagenome
Binning
Long reads
Assembly
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Summary: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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ISSN:1474-760X
1474-7596
1474-760X
DOI:10.1186/s13059-019-1834-9