[ged] Nov 22, 1 PM, GED Journal Club, Adina

[Adina Chuang Howe]

I'll be presenting the following paper and commenting on our
partitioning approach on their dataset (hopefully!).
Thanks,
Adina

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Individual genome assembly from complex community short-read
metagenomic datasets
Luo et al. (The PI is a former Tiedje Lab PhD student)
Assembling individual genomes from complex community metagenomic data
remains a challenging issue for environmental studies. We evaluated
the quality of genome assemblies from community short read data
(Illumina 100 bp pair-ended sequences) using datasets recovered from
freshwater and soil microbial communities as well as in silico
simulations. Our analyses revealed that the genome of a single
genotype (or species) can be accurately assembled from a complex
metagenome when it shows at least about 20 􏰀 coverage. At lower
coverage, however, the derived assemblies contained a substantial
fraction of non-target sequences (chimeras), which explains, at least
in part, the higher number of hypothetical genes recovered in
metagenomic relative to genomic projects. We also provide examples of
how to detect intrapopulation structure in metagenomic datasets and
estimate the type and frequency of errors in assembled genes and
contigs from datasets of varied species complexity.
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