Improving the Accuracy of Genome Assemblies


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 v1.0.2 releasedAugust 24, 2012


We've released SEQuel v1.0.2, with updates adding several functional features and fixing some existing bugs. Thanks to Dmitry Antipov and others at the Algorithmic Biology Lab in Saint Petersburg, Russia, for their valuable suggestions and comments.

Journal ArticleJune 11, 2012


Our manuscript describing SEQuel was published in the journal of Bioinformatics.

SEQuel v1.0.1 releasedMarch 17, 2012


The first public release of SEQuel is now available for download. For instructions on how to setup and run the programs, see our manual page.

PublicationMarch 16, 2012

The SEQuel manuscript was accepted for publication in ISMB 2012.