Optimizing sequencing protocols for leaderboard metagenomics by combining long and short reads
| Autor: | Jason Dang, Timothy D. Arthur, Zhenjiang Zech Xu, Rodolfo A. Salido, Cameron Martino, Rob Knight, James Gaffney, Jon G. Sanders, Mahdieh Khosroheidari, Greg Humphrey, Jeremiah J. Minich, Brigid S. Boland, Kristen Jepsen, Qiyun Zhu, John T. Chang, Marlon Liyanage, Pieter C. Dorrestein, Robert A. Quinn, Douglas Conrad, Karenina Sanders, Caitriona Brennan, Feng Chen, William J. Sandborn, Marcus W. Fedarko, Cliff Green, Larry Smarr, Pavel A. Pevzner, Anton Bankevich, Tariq M. Rana, Sergey Nurk, Vanessa V. Phelan |
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| Jazyk: | angličtina |
| Rok vydání: | 2019 |
| Předmět: |
lcsh:QH426-470
Bioinformatics Library preparation Assembly Method Computational biology Biology Long reads Benchmark Genome 03 medical and health sciences Mice 0302 clinical medicine Human gut Information and Computing Sciences Genetics Animals Humans lcsh:QH301-705.5 030304 developmental biology 0303 health sciences Genomic Library Human Genome High-Throughput Nucleotide Sequencing Binning Biological Sciences 3. Good health Gastrointestinal Microbiome Benchmarking lcsh:Genetics lcsh:Biology (General) Metagenomics Leaderboard metagenome 030217 neurology & neurosurgery Environmental Sciences |
| Zdroj: | Genome Biology, Vol 20, Iss 1, Pp 1-14 (2019) Genome biology, vol 20, iss 1 Genome Biology |
| DOI: | 10.1186/s13059-019-1834-9 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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