Journal
BIOINFORMATICS
Volume 23, Issue 21, Pages 2942-2944Publisher
OXFORD UNIV PRESS
DOI: 10.1093/bioinformatics/btm451
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Funding
- NIGMS NIH HHS [R01 GM066025, R01GM066025] Funding Source: Medline
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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 Illuminas Solexa Sequencing, produce high genomic coverage by generating a very large number of small reads (similar to 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.
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