Section: New Software and Platforms

High throughput sequence comparisons

Participants : Sébastien Brillet, Erwan Drezen, Dominique Lavenier, Pierre Peterlongo, Ivaylo Petrov.

KLAST: bank-to-bank alignment search tool

KLAST is a fast, accurate and NGS scalable bank-to-bank sequence similarity search tool providing significant accelerations of seeds-based heuristic comparison methods, such as the Blast suite. KLAST is a new optimized implementation of the PLAST algorithm to which several improvements have been made in 2014. KLAST is fully designed to compare query and subject comprised of large sets of DNA, RNA and protein sequences. It is significantly faster than original PLAST, while providing comparable sensitivity to BLAST and SSearch algorithms. KLAST contains a fully integrated data-filtering engine capable of selecting relevant hits with user-defined criteria (E-Value, identity, coverage, alignment length, etc.). Klast is developed with the Korilog Company and an academic version is now freely available for the scientific community [contact: D. Lavenier]. [34] https://koriscale.inria.fr/klast/

COMMET: de novo comparison of metagenomic datasets

Commet is an extension of the Comparead tool that proposes to compute similarity between set of raw non assembled (and usually non-assemblable with current state of the art assemblers) reads. Commet enables to factorize computations when n read sets have to be compared all together. Moreover, Commet proposes a new representation of sub-read sets that has the main advantages to save huge disk space and to enable efficient logical operations between sub-read sets. [contact: P. Peterlongo] https://colibread.inria.fr/software/commet/