23 citations
0 runs

classify_metagenome

By Ounit R., Last update 1494699000
All tools Run in Terminal

classify_metagenome description

Classify_metagenome wrapper for CLARK allows to classify metagenomic samples against several databases of user choice. Use can choose among Bacteria, Viruses genomes (from NCBI/RefSeq), and Human (latest GRCh38). They will be downloaded automatically if needed. In addition, user can choose any database uploaded locally to a designated folder


Parent program: CLARK

CLARK is a versatile, fast and accurate sequence classification tool, especially useful for metagenomics and genomics applications. ClARK uses a novel approach to classify metagenomic reads at the species or genus level with high accuracy and high speed. Extensive experimental results on various metagenomic samples show that the classification accuracy of CLARK is better or comparable to the best state-of-the-art tools and it is significantly faster than any of its competitors. In its fastest single-threaded mode CLARK classifies, with high accuracy, about 32 million metagenomic short reads per minute. CLARK can also classify BAC clones or transcripts to chromosome arms and centromeric regions.