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39 lines
1.9 KiB
Text
39 lines
1.9 KiB
Text
This is Ugene's (http://ugene.net/) fork of the CLARK tool
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(http://clark.cs.ucr.edu/Tool/), with supports building DB directly from
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gzip & 7z packed RefSeq files
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CLARK: CLAssifier based on Reduced K-mers
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The problem of DNA sequence classification is central to several
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application domains in molecular biology, genomics, metagenomics and
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genetics. The problem is computationally challenging due to the size of
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datasets generated by modern sequencing instruments and the growing size
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of reference sequence databases.
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CLARK is a novel method for supervised sequence classification based on
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discriminative k-mers. Somewhat unique among other metagenomic and
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genomic classification methods, CLARK provides a confidence score for
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its assignments which can be used in downstream analysis. The utility of
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CLARK is demonstrated on two distinct specific classification problems:
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1) the assignment of metagenomic reads to known bacterial genomes
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2) the assignment of BAC clones and transcript to chromosome arms (in
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the absence of a finished assembly for the reference genome).
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Three classifiers or variants in the CLARK framework are provided :
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CLARK (default): created for powerful workstation, it may require a
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significant amount of RAM to run with large database (e.g., all
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bacterial genomes from NCBI/RefSeq). This classifier queries k-mers
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with exact matching.
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CLARK-l (light): created for workstations with limited memory, this
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software tool provides precise classification on small metagenomes.
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Indeed, for metagenomics analysis, CLARK-l works with a sparse or
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"light" database (up to 4 GB of RAM) that is built using distant and
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non-overlapping k-mers. This classifier queries k-mers with exact
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matching.
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CLARK-S (spaced): created for powerful workstation exploiting spaced k-
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mers, this classifier requires a higher RAM usage than CLARK or CLARK-l,
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but it does offer a higher sensitivity. CLARK-S completes the CLARK
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series of classifiers.
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