Section: New Software and Platforms

Sequence comparison

PLAST: Parallel Local Alignment Search Tool

PLAST 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. PLAST is fully designed to compare query and subject comprised of large sets of DNA, RNA and protein sequences. It is significantly faster than BLAST, while providing comparable sensitivity. PLAST contains a fully integrated data-filtering engine capable of selecting relevant hits with user-defined criteria (E-Value, identity, coverage, alignment length, etc.).

Contact: Dominique Lavenier

URL: https://plast.inria.fr

SIMKA: Comparison of metagenomic datasets

Simka rapidly compares a large number of metagenomics datasets using efficient kmer-based method. Datasets may contains hundreds of millions of NGS sequences. Kmers of each datasets are rapidly counted and identified to estimate the pairwise similarities between datasets. The output of Simka can be used for clustering purpose or for checking correlation between metadata.

Contact: Gaëtan Benoit

URL: https://gatb.inria.fr/software/simka/

BGREAT: read mapper on de-Bruijn graph

BGREAT maps reads on a de-Bruijn Graph, usually used for genome assembly. Mapping reads on graphs offers the possibility to conserve all the pieces of information lost during the assembly process and to avoid multi-mapping problems due to genomic repeats. BGREAT rewrites a read sequence as a succession of unitigs sequences. It can map millions of reads per CPU hour on a de-Bruijn graph built from a large set of human genomic reads.

Contact: Antoine Limasset

URL: http://github.com/Malfoy/BGREAT/