1. Extending assembly of short DNA sequences to handle error
- Author
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Josephine A. Reinhardt, Elaine R. Mardis, Jeffery L. Dangl, Corbin D. Jones, Matthew T. Hickenbotham, Vincent Magrini, William R. Jeck, and David A. Baltrus
- Subjects
Statistics and Probability ,Sequence analysis ,Molecular Sequence Data ,2 base encoding ,Sequence assembly ,Hybrid genome assembly ,Computational biology ,Biology ,Sensitivity and Specificity ,Biochemistry ,Genome ,DNA sequencing ,Deep sequencing ,Consensus Sequence ,Molecular Biology ,Genetics ,Base Sequence ,Chromosome Mapping ,Reproducibility of Results ,DNA ,Sequence Analysis, DNA ,Computer Science Applications ,Computational Mathematics ,Computational Theory and Mathematics ,k-mer ,Artifacts ,Sequence Alignment ,Algorithms - Abstract
Inexpensive de novo genome sequencing, particularly in organisms with small genomes, is now possible using several new sequencing technologies. Some of these technologies such as that from Illumina's Solexa Sequencing, produce high genomic coverage by generating a very large number of small reads (∼30 bp). While prior work shows that partial assembly can be performed by k-mer extension in error-free reads, this algorithm is unsuccessful with the sequencing error rates found in practice. We present VCAKE (Verified Consensus Assembly by K-mer Extension), a modification of simple k-mer extension that overcomes error by using high depth coverage. Though it is a simple modification of a previous approach, we show significant improvements in assembly results on simulated and experimental datasets that include error.Availability: http://152.2.15.114/~labweb/VCAKEContact: william.jeck@gmail.com
- Published
- 2007
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