A Method and Software Significantly Improving the Accuracy Of Genome Assemblies: SEQuel
Removed 35% to 96% of small-scale assembly errors. Introduced positional de Bruijn graph for contig refinement. Demonstrated utility in hard (single-cell) assembly. SEQuel can be used in combination with any NGS assembler.
Correcting errors in contigs from high throughput sequencing (HTS) assemblies. These might include bacterial/plant/vertebrate genomes that were not been previously sequenced, or the products of transcript assembly.
UCSD researchers have recently developed a method and companion software, SEQuel, to correct errors (i.e., insertions, deletions, and substitution errors) in the assembled contigs of NGS data. Fundamental of SEQuel is the positional de Bruijn graph, a graph structure that models k-mers within reads while incorporating the approximate positions of reads into the model. SEQuel takes as input an assembled contig, the paired-end reads that align to that contig and the approximate positions where they aligned, and returns a refined contig.
State Of Development The development stage of SEQuel is complete, and initial tests on several datasets have already shown its utility in correcting errors in assembled genomes. When SEQuel was applied to the recently assembled Deltaproteobacterium SAR324 genome, which is the first bacterial genome with a comprehensive single-cell genome assembly, and it made over 800 changes (insertions, deletions and substitutions) to refine this assembly. Related Materials Tech ID/UC Case 22625/2013-803-0 Related Cases 2013-803-0
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