SEQuel: Refine of a Genome Assembly

SEQuel is a tool for correcting errors (i.e., insertions, deletions, and substitutions) in contigs output from assembly. Built by Roy Ronen and Christina Boucher in Pavel Pevzner's lab, there are several exciting extensions to the work. 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. For more information see the SEQuel website. There are several possible projects that extend this work.