[metagenomics-jclub] Journal Club, Wed, PSB271 10 AM

[Adina Chuang Howe]

Titus will be talking about something (as described below).  :)  We'll
meet at 10 AM -- note the earlier time!

Cheers, Adina

Soil metagenome assembly: diverse data, diverse challenges

Soil contains one of the most diverse and unexplored microbial populations
on the planet.  As part of the Great Prairie DOE project, the JGI has generated
several terabases (10**12) of whole metagenome shotgun sequence from a number
of sites in the midwest.  Assembling this data into something meaningful has
been challenging, because it stretches current computational capacity and
algorithms.  We've developed a range of approaches based on a synopsis
data structure, the Bloom filter, that lets us explore and analyze extremely
large k-mer assembly graphs, and do high-quality pre-filtering for de Bruijn
graph assemblers.  This has led us to a better understanding of sequence
assembly approaches, Illumina artifacts, and assembly scaling.  These results
have also enabled us to assemble very large mRNAseq data sets from emerging
model organisms.