[ged] Journal Club next week

[Jason Pell]

Hi everyone,

QP will be presenting the paper tomorrow for journal club. 11am in 2228.

Jason

On Tue, Mar 6, 2012 at 8:25 PM, Qingpeng Zhang <qingpeng at msu.edu> wrote:
> I will be presenting the paper "Assessment of metagenomic assembly
> using simulated next generation sequencing data." in next
> week's journal club.
>
> http://www.ncbi.nlm.nih.gov/pubmed/22384016
>
> Assessment of metagenomic assembly using simulated next generation
> sequencing data.
> Mende DR, Waller AS, Sunagawa S, Järvelin AI, Chan MM, Arumugam M,
> Raes J, Bork P.
>
> European Molecular Biology Laboratory, Heidelberg, Germany.
> Abstract
> Due to the complexity of the protocols and a limited knowledge of the
> nature of microbial communities, simulating metagenomic sequences
> plays an important role in testing the performance of existing tools
> and data analysis methods with metagenomic data. We developed
> metagenomic read simulators with platform-specific (Sanger,
> pyrosequencing, Illumina) base-error models, and simulated metagenomes
> of differing community complexities. We first evaluated the effect of
> rigorous quality control on Illumina data. Although quality filtering
> removed a large proportion of the data, it greatly improved the
> accuracy and contig lengths of resulting assemblies. We then compared
> the quality-trimmed Illumina assemblies to those from Sanger and
> pyrosequencing. For the simple community (10 genomes) all sequencing
> technologies assembled a similar amount and accurately represented the
> expected functional composition. For the more complex community (100
> genomes) Illumina produced the best assemblies and more correctly
> resembled the expected functional composition. For the most complex
> community (400 genomes) there was very little assembly of reads from
> any sequencing technology. However, due to the longer read length the
> Sanger reads still represented the overall functional composition
> reasonably well. We further examined the effect of scaffolding of
> contigs using paired-end Illumina reads. It dramatically increased
> contig lengths of the simple community and yielded minor improvements
> to the more complex communities. Although the increase in contig
> length was accompanied by increased chimericity, it resulted in more
> complete genes and a better characterization of the functional
> repertoire. The metagenomic simulators developed for this research are
> freely available.
>
>
> Sincerely yours,
>
> Qingpeng Zhang
> Ph.D. Student
> GED Lab in 2228 BPS Building
> Department of Computer Science and Engineering
> Michigan State University
> East Lansing, MI 48824
>
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