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FreClu | Frequency-based de novo short-read clustering for error trimming in NGS

Focuses on the broad parent–child relationships hidden in a set of short reads generated from identical experiments with the same starting points. FreClu establishes a novel framework for correcting sequencing errors in short reads by consulting the inherent relationships among an entire set of reads. This short-read clustering method was designed to perform an essential function in de novo transcript identification and genome assembly with deep coverage.

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FreClu specifications

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FreClu distribution


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  • Shinichi Morishita <>


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Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan; Department of Molecular Preventive Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan; Bioinformatics Research and Development (BIRD), Japan Science and Technology Agency (JST), Tokyo, Japan

Funding source(s)

This work was supported in part by a Grant-in-Aid for Scientific Research on Priority Areas from the Ministry of Education, Culture, Sports, Science and Technology of Japan, and by a grant for Bioinformatics Research and Development (BIRD) from the Japan Science and Technology Agency (JST).

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