COSINE: non-seeding method for mapping long noisy sequences.
Identifieur interne : 000D74 ( PubMed/Checkpoint ); précédent : 000D73; suivant : 000D75COSINE: non-seeding method for mapping long noisy sequences.
Auteurs : Pegah Tootoonchi Afshar [États-Unis] ; Wing Hung Wong [États-Unis]Source :
- Nucleic acids research [ 1362-4962 ] ; 2017.
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- MESH :
- methods : Computational Biology, High-Throughput Nucleotide Sequencing, Sequence Alignment.
- statistics & numerical data : High-Throughput Nucleotide Sequencing.
- Algorithms, Base Sequence, Reproducibility of Results, Software.
Abstract
Third generation sequencing (TGS) are highly promising technologies but the long and noisy reads from TGS are difficult to align using existing algorithms. Here, we present COSINE, a conceptually new method designed specifically for aligning long reads contaminated by a high level of errors. COSINE computes the context similarity of two stretches of nucleobases given the similarity over distributions of their short k-mers (k = 3-4) along the sequences. The results on simulated and real data show that COSINE achieves high sensitivity and specificity under a wide range of read accuracies. When the error rate is high, COSINE can offer substantial advantages over existing alignment methods.
DOI: 10.1093/nar/gkx511
PubMed: 28586438
Affiliations:
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Here, we present COSINE, a conceptually new method designed specifically for aligning long reads contaminated by a high level of errors. COSINE computes the context similarity of two stretches of nucleobases given the similarity over distributions of their short k-mers (k = 3-4) along the sequences. The results on simulated and real data show that COSINE achieves high sensitivity and specificity under a wide range of read accuracies. When the error rate is high, COSINE can offer substantial advantages over existing alignment methods.</AbstractText><CopyrightInformation>© The Author(s) 2017. 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