Meteor (“Metagenome: each one of reads”)
Remove duplicate reads from huge metagenomes. Combined with Commet, it will provide informations about α and β-diversity, in progress.
Commet (“Compare multiple metagenomes”)
Provides a global similarity overview between all datasets of a large metagenomic project, directly from non-assembled reads, described in .
Extract similar reads between two potentially huge metagenomic datasets, described in .
 N. Maillet, G. Collet, T. Vannier, D. Lavenier, P. Peterlongo, Commet: comparing and combining multiple metagenomic datasets, Bioinformatics and Biomedicine (BIBM) (Acceptance ratio: 19%), IEEE International Conference, Belfast (Nov. 2014) [PDF] [Webpage]
 K. R. Bradnam, J. N. Fass, A. Alexandrov, P. Baranay, M. Bechner et al., Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species, Gigascience (Jan. 2013) [Open-access]
 N. Maillet, C. Lemaitre, R. Chikhi, D. Lavenier, P. Peterlongo, Compareads: comparing huge metagenomic experiments, BMC Bioinformatics (Dec. 2012) [Open-access] [Webpage]
 S. Renaut, N. Maillet, E. Normandeau, C. Sauvage, N. Derome, S. M. Rogers, L. Bernatchez, Genome-wide patterns of divergence during speciation: the lake whitefish case study, Philosophical Transactions of the Royal Society B: Biological Sciences (Feb. 2012) [Open-access]
 D. Earl, K. Bradnam, J. St John, A. Darling, D. Lin et al., Assemblathon 1: a competitive assessment of de novo short read assembly methods, Genome Research (Dec. 2011) [Open-access]
Best poster among 112 in JOBIM conference, 2012. Compareads: comparing huge metagenomic experiments [PDF]
N. Maillet, De novo comparision of huge metagenomic experiments coming from NGS technologies : application on Tara Oceans project, PhD Thesis, 2010-2013 [PDF (fr)]