一个新的宏基因组分类器KrakenUniq
  • KrakenUniq使用特有的k -mer计数提高物种鉴定的准确性和降低分类器误报(假阳性);
  • 在基准化测试中,KrakenUniq在分类宏基因组数据方面比Blast,Diamond和MetaFlow 等现有方法表现更好;
  • 由于代码的改进,KrakenUniq通常比Kraken运行的更快,约提高了50%,内存需求则几乎一样;
  • KrakenUniq还实现了菌株水平或更细级别的菌株鉴定,且提高了对病毒序列的识别能力,同时还可以对多个数据库进行分层搜索。
主编推荐语
高春辉
KrakenUniq可被视为是在Kraken基础上附加了k-mer信息之后的一个改进型。
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Genome Biology [IF:10.806]

KrakenUniq: confident and fast metagenomics classification using unique k-mer counts

KrakenUniq:使用特有K-mer计数进行准确和快速的宏基因组分类

10.1186/s13059-018-1568-0

2018-11-16, Article

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False-positive identifications are a significant problem in metagenomics classification. We present KrakenUniq, a novel metagenomics classifier that combines the fast k-mer-based classification of Kraken with an efficient algorithm for assessing the coverage of unique k-mers found in each species in a dataset. On various test datasets, KrakenUniq gives better recall and precision than other methods and effectively classifies and distinguishes pathogens with low abundance from false positives in infectious disease samples. By using the probabilistic cardinality estimator HyperLogLog, KrakenUniq runs as fast as Kraken and requires little additional memory. KrakenUniq is freely available at https://github.com/fbreitwieser/krakenuniq .

First Authors:
F P Breitwieser

Correspondence Authors:
F P Breitwieser,S L Salzberg

All Authors:
F P Breitwieser,D N Baker,S L Salzberg

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