Ab initio whole genome shotgun assembly with mated short reads
RECOMB'08 Proceedings of the 12th annual international conference on Research in computational molecular biology
IDBA: a practical iterative de bruijn graph de novo assembler
RECOMB'10 Proceedings of the 14th Annual international conference on Research in Computational Molecular Biology
PERGA: A Paired-End Read Guided De Novo Assembler for Extending Contigs Using SVM Approach
Proceedings of the International Conference on Bioinformatics, Computational Biology and Biomedical Informatics
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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 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/VCAKE Contact: william.jeck@gmail.com