对Illumina数据进行实时宏基因组分类的新方法
创作:高春辉 审核:szx 2018年06月23日
  • LiveKraken接受Illumina测序仪的实时原始数据流,并依据物种来源不同将这些数据进行分类;
  • 在既有的Kraken工具基础上开发,当测序完成时二者所得结果完全一致;
  • LiveKraken的优势是在测序的早期也能得到与完成时类似的结果,最多可以争得一周的时间,且数据累积越多越精确;
  • 提供了可执行文件安装和Conda方式两种部署方式;
  • 和Kraken相比,LiveKraken有轻微性能损失,但在紧急实验中,LiveKraken将具有明显的时间优势。
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Bioinformatics上发表的最新研究,介绍了一种对Illumina数据进行实时宏基因组分类的新工具——LiveKraken,可依据物种来源不同将原始数据进行分类。
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Bioinformatics [IF:5.61]

LiveKraken - Real-time metagenomic classification of Illumina data

LiveKraken:Illumina数据的实时宏基因组分类

10.1093/bioinformatics/bty433

2018-06-01, Article

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Motivation: In metagenomics, Kraken is one of the most widely used tools due to its robustness and speed. Yet, the overall turnaround time of metagenomic analysis is hampered by the sequential paradigm of wet and dry lab. In urgent experiments, it can be crucial to gain a timely insight into a dataset.
Results: Here, we present LiveKraken, a real-time read classification tool based on the core algorithm of Kraken. LiveKraken uses streams of raw data from Illumina sequencers to classify reads taxonomically. This way, we are able to produce results identical to those of Kraken the moment the sequencer finishes. We are furthermore able to provide comparable results in early stages of a sequencing run, allowing saving up to a week of sequencing time on an Illumina HiSeq in High Throughput Mode. While the number of classified reads grows over time, false classifications appear in negligible numbers and proportions of identified taxa are only affected to a minor extent.
Availability: LiveKraken is available at https://gitlab.com/rki_bioinformatics/LiveKraken.
Contact: renardb@rki.de.

First Authors:
Simon H Tausch

Correspondence Authors:
Bernhard Y Renard

All Authors:
Simon H Tausch,Benjamin Strauch,Andreas Andrusch,Tobias P Loka,Martin S Lindner,Andreas Nitsche,Bernhard Y Renard

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