SEQuel

SEQuel is a tool for correcting errors (i.e., insertions, deletions, and substitutions) in contigs output from assembly. While assemblies of next generation sequencing (NGS) data are accurate, they still contain a substantial number of errors that need to be corrected after the assembly process. The algorithm behind SEQuel makes use of a graph structure called the positional de Bruijn graph, which models k-mers within reads while incorporating their approximate positions into the model. SEQuel substantially reduces the number of small insertions, deletions and substitusion erros in assemblies of both standard (multi-cell) and single-cell sequencing data. SEQuel was tested mainly on Illumina sequence data, in combination with multiple NGS assemblers, such as Euler-SR, Velvet, SoapDeNovo, ALLPATHS and SPAdes.

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  1. Carugo, Oliviero (ed.); Eisenhaber, Frank (ed.): Data mining techniques for the life sciences (2016)