Seminars – Metagenomic assembly through the lens of validation: recent advances in assessing and improving the quality of genes and genomes assembled from metagenomes

EVENT : C3BI Seminars

Metagenomic assembly through the lens of validation: recent advances in assessing and improving the quality of genes and genomes assembled from metagenomes


Main speaker : Todd Treangen, from Center for Bioinformatics and Computational Biology – Computer Science Department, University of Maryland Date : 05/07/2017 at 02:00 pm Location : Auditorium Francois Jacob – BIME (26) ,Institut Pasteur, Paris


Metagenomic assembly through the lens of validation: recent advances in assessing and improving the quality of genes and genomes assembled from metagenomes

Metagenomic samples are snapshots of complex ecosystems at work. These samples often involve hundreds of known and unknown species, contain multiple strain variants, and vary greatly both within environments and across environments. Metagenomic assembly is a fundamental tool for elucidating microbial ecology behind these dynamic communities. Specifically, metagenome assembly allows us to reconstruct genes and genomes from metagenomes. Genes and genomes are on two ends of the assembly spectrum, the former often represents the minimal continuous region that is desired, and the later, the optimal result; one contig per replicon. Multiple metagenomic assembly strategies, pipelines, and assemblers have appeared in recent years; several of these have been substantially improved upon the original heuristics and algorithms employed nearly a decade ago designed to solve this challenging computational problem. However, due to the inherent complexity of the metagenome assembly problem, regardless of the assembly algorithm and sequencing method, metagenome assemblies contain errors. In this talk I will cover three main topics: 1) recent progress in de novo assembly of metagenomes, 2) reference-guided assembly of metagenomes with MetaCompass, and 3) de novo metagenomic assembly mis-assembly detection with VALET.


Due to security policy in Institut Pasteur, please register before if you plan to come to this meeting