GATB: Genome Assembly & Analysis Tool Box

Erwan Drezen, Guillaume Rizk, Rayan Chikhi, Charles Deltel, Claire Lemaitre, Pierre Peterlongo, Dominique Lavenier
2014 Computer applications in the biosciences : CABIOS  
Comparative metagenomics aims to provide high-level information based on DNA material sequenced from different environments. The purpose is mainly to estimate proximity between two or more environmental sites at the genomic level. One way to estimate similarity is to count the number of similar DNA fragments. From a computational point of view, the problem is thus to calculate the intersections between datasets of reads. Resorting to traditional methods such as all-versus-all sequence alignment
more » ... is not possible on current metagenomic projects. For instance, the Tara Oceans project involves hundreds of datasets of more than 100M reads each.
doi:10.1093/bioinformatics/btu406 pmid:24990603 pmcid:PMC4184257 fatcat:lruwdsxsbvf2neaixo6ugzzfk4