FreClu statistics

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FreClu specifications


Unique identifier OMICS_01048
Name FreClu
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes


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  • person_outline Shinichi Morishita <>

Publication for FreClu

FreClu in pipeline

PMCID: 4719071
PMID: 26026159
DOI: 10.1093/bib/bbv029

[…] of positions disregarded in the sorting of each copy determines the hamming distance allowed. a similar approach in the msa tools coral [] and echo [] is the use of adjacency lists. and finally, freclu [] and an unnamed tool by aita et al. [] cluster reads by their hamming distance and then use different error correction strategies on the resulting neighbourhoods (i.e. the clusters)., […]

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FreClu in publications

PMCID: 3923269
PMID: 24138055
DOI: 10.1186/1471-2229-13-164

[…] denotes the number of filtered sequences that exactly matched the experimentally designed sequence pattern., to further reduce complexity, we performed a clustering analysis using the program freclu []. this analysis revealed that the library samples consisted of a large number of individual sequences, which could not be clustered. in contrast, the chip samples showed clustering above 40% […]

PMCID: 3485269
PMID: 23118865
DOI: 10.1371/journal.pone.0047043

[…] sequencing assay with 8 samples per lane generated on average 2.3 million raw reads for each sample. raw reads were preprocessed with a frequency-based short-read clustering algorithm called freclu (default parameters), where raw reads were quality filtered, adaptor trimmed, replicated reads merged and sequencing-error corrected. freclu generated on average approximately 0.4 million […]

PMCID: 3258298
PMID: 22168751
DOI: 10.1186/1471-2164-12-605

[…] and sequencing methods., solexa sequencing are known for its short reads, and errors can be pervasive in short-read sequencing []. to address this concern, we clustered the raw reads using the freclu software [], which takes the read count into consideration. the results showed that this clustering process can improve the accuracy of short reads mapping (table ). however, […]

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FreClu institution(s)
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
FreClu 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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