期刊
BIOLOGY DIRECT
卷 13, 期 -, 页码 -出版社
BMC
DOI: 10.1186/s13062-018-0220-y
关键词
Metagenome; MetaSUB; Sequence classification
类别
资金
- National Natural Science Foundation of China [61472246]
- National Basic Research Program of China [2013CB956103]
- National High-Tech RD Program (863) [2014AA021502]
Background: Many methods have been developed for metagenomic sequence classification, and most of them depend heavily on genome sequences of the known organisms. A large portion of sequencing sequences may be classified as unknown, which greatly impairs our understanding of the whole sample. Result: Here we present MetaBinG2, a fast method for metagenomic sequence classification, especially for samples with a large number of unknown organisms. MetaBinG2 is based on sequence composition, and uses GPUs to accelerate its speed. A million 100 bp Illumina sequences can be classified in about 1 min on a computer with one GPU card. We evaluated MetaBinG2 by comparing it to multiple popular existing methods. We then applied MetaBinG2 to the dataset of MetaSUB Inter-City Challenge provided by CAMDA data analysis contest and compared community composition structures for environmental samples from different public places across cities. Conclusion: Compared to existing methods, MetaBinG2 is fast and accurate, especially for those samples with significant proportions of unknown organisms. Reviewers: This article was reviewed by Drs. Eran Elhaik, Nicolas Rascovan, and Serghei Mangul.
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