FreClu - FREquencing based de Novo short read CLUstering | Tool name | FreClu - FREquencing based de Novo short read CLUstering |
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| URL | http://mlab.cb.k.u-tokyo.ac.jp/~quwei/DeNovoShortReadClustering/ |
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| Important features | 1. Novel, massively parallel sequencing technologies provide a highly detailed structure of transcriptome and genome by yielding deep coverage of short reads, though their utility is interfered due to a considerable sequencing quality problem and short length of reads.
2. Sequencing-error trimming in short reads is therefore a vital process which could improve the successful rate of reference mapping as well as polymorphorism detection.
3. This algorithm organizes erroneous short sequences, originating in a single abundant sequence into a tree structure such that each child sequence is considered to be derived stochastically from its more abundant parent sequence because of sequencing errors. |
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| Citations | Qu W, Hashimoto S, Morishita S. Efficient frequency-based de novo short-read clustering for error trimming in next-generation sequencing. Genome Res. 2009
Jul;19(7):1309-15. Epub 2009 May 13. PubMed PMID: 19439514; PubMed Central PMCID:
PMC2704438. |
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| Year of publication | 2009 |
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| Rank by usage frequency | 100 |
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| Comments | |
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| Function | RNA seq alignment |
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| Category | Free, Downloadable |
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| Input file format | seq.txt, qseq.txt, FASTQ |
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| Output file format | Text |
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