RGASP3/dnGASP

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The "Sequence Mapping and Assembly Assessment Project (SMAAP) RGASP3/dnGASP" is a collaborative effort among researchers to compare and evaluate methods and strategies for de novo genome assembly and RNASeq read alignment using data from 2nd generation sequencing platforms.  

 

 Two common datasets will be made available to the participants in early November: 

 

-        Data for de novo assembly: simulated sequence reads from a high-throughput sequencing platform derived from a large (~2Gb) synthetic diploid genome. (Already available at the cnag.bsc.es)

-        Data for RNASeq read alignment will be available for download from the Sanger Institute.

 

The mappings or alignments of both datasets will be submitted by participants before February 15th, 2011.  (check the web sites above for definitive submission dates). The required submission formats will be provided soon and can be obtained from the RGASP3 and dnGASP web sites.  

 

The submitted results will be evaluated by the SMAAP organizers using a standardized metrics to compare the different approaches. During the workshop each participating group will present their method and an evaluation of their submission. Additionally, there would be 5 keynote presentations by selected speakers and 2 wrap-up presentations by the Evaluation Committee.

 

The principal aim of the workshop is to allow a full and fair evaluation of different analysis methods to:

-        Generate high-quality de novo genome assemblies for large eukaryotic genome from short-read sequence data.   

-        Generate high-quality RNASeq read alignments that can be used for efficient transcriptome characterization: transcript discovery and quantitation.  

 

Proposed calendar for workshop on the comparison and evaluation of bioinformatic tools for 2nd generation sequencing data mapping and assembly:

 

-        Mid-September 2010: the SMAAP meeting will be announced at the Genome Informatics meeting (Wellcome Trust Genome Campus, Hinxton, Cambridge, UK)

-        November 2010: two 2nd generation sequencing datasets will be made available to the research community through the dnGASP and RGASP3 project portals.

-        November 2010-February 2011: participants will submit their assembly and mapping results using the two datasets

-        January-February 2011: data evaluation by the dnGASP and RGASP3 evaluation committees

-        April 5-7th 2011: CIDC meeting (SMAAP workshop)

 

Please watch this page or contact Roderic Guigo (CRG) or Ivo Gut (CNAG) for more information.

 

This meeting will be organized in partnership with the International Center for Scientific Debate (CIDC), an initiative fostered by Biocat together with “la Caixa” Foundation Welfare Projects.