[BBC] [Gtpb] Bioinformatics Training Course Announcement

[Pedro Fernandes]

                Course Announcement

NOTE: please apply as soon as possible, the period for applications is  
exceptionally short due to operational reasons

*ARANGS13*
Automated and reproducible analysis of NGS data

   IMPORTANT DATES for ARANGS13
    Deadline for applications: October 8th 2013
    Notification of acceptance dates: October 15th 2013
    Course date: October 21st - October 24th 2013

Course Description:
Next generation sequencing (NGS) technologies for DNA have resulted in  
a yet bigger deluge of data. Researchers are learning that analysing  
such data sets is becoming the bottleneck in their work. In many  
cases, several steps in these analyses are fairly generic (e.g.  
quality control filtering, alignment to reference sequences, typing)  
so that off-the-shelf pipelines can be applied. In other cases, novel  
research approaches require development of new analysis pipelines.  
Either way, all analysis steps should be repeatable and any changes  
made to the data (e.g. renaming, annotation, alignment) should be  
recorded so that the provenance of the results is clear and inferences  
are reproducible. In this brief workshop we will establish several  
best practices of reproducibility and provenance recording in the  
(comparative) analysis of data obtained by NGS. In doing so we will  
encounter the commonly used technologies that enable these best  
practices by working through use cases that illustrate the underlying  
principles. Building on the basis of workflow development, we will  
further illustrate how custom-built workflows can be manipulated using  
graphical platforms (e.g. Galaxy, Taverna, etc.).

Best practices

     Standardized project organization
     Projects 'runnable' without user intervention
     No loss of data, metadata, parameters or source code through versioning
     Sharing of scripts and workflows

Technologies

     Next generation sequencing platforms
     File formats (e.g. FASTQ, SAM/BAM, GFF3)
     Command-line executables, command line scripting and batching
     High-level programming with domain-specific toolkits
     Revision control systems
     Workflow environments (both visual and command line)

Use cases

     Phylogenetic placement of metagenomic data
     Typing of pathogens
     Comparative analysis of multicellular genomic data
     Post-assembly: handling richly annotated genomes

More information, including application instructions, available at
http://gtpb.igc.gulbenkian.pt/bicourses/ARANGS13/

Thank you
Pedro Fernandes
GTPB coordinator


--
Pedro Fernandes
Instituto Gulbenkian de Ciência
Apartado 14
2781-901 OEIRAS
PORTUGAL
Tel +351 21 4407912
http://gtpb.igc.gulbenkian.pt





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