MetaProb

Metagenomic reads binning with spaced seeds. The growing number of sequencing projects in medicine and environmental sciences is creating new computational demands in the analysis and processing of these very large datasets. Recently we have proposed an algorithm called MetaProb that can accurately cluster metagenomic reads with a precision that is currently unmatched. The competitive advantage of MetaProb depends on the use of sequence signatures based on contiguous $k$-mers. Instead of using contiguous $k$-mers, in this work we explore the use of spaced seeds where mismatches are allowed at carefully predetermined positions. The experimental results show that the use of mismatches can further improve the accuracy and decrease the memory requirements. Availability: {url https://bitbucket.org/samu661/metaprob.}

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