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.



SEQuel: improving the accuracy of genome assemblies.
R. Ronen, C. Boucher, H. Chitsaz, and P. Pevzner.
Bioinformatics (2012) 28 (12): i188-i196