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- Title
LiveKraken––real-time metagenomic classification of illumina data.
- Authors
Tausch, Simon H; Andrusch, Andreas; Strauch, Benjamin; Loka, Tobias P; Lindner, Martin S; Renard, Bernhard Y; Nitsche, Andreas
- Abstract
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 and implementation LiveKraken is available at https://gitlab.com/rki%5fbioinformatics/LiveKraken. Supplementary information Supplementary data are available at Bioinformatics online.
- Subjects
METAGENOMICS; DATA analysis; NUCLEOTIDE sequencing; NUCLEOTIDE analysis; COMMAND-line interfaces
- Publication
Bioinformatics, 2018, Vol 34, Issue 21, p3750
- ISSN
1367-4803
- Publication type
Article
- DOI
10.1093/bioinformatics/bty433