Question: Bioinformatics Training Course In Portugal
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gravatar for Pedro Fernandes
5.0 years ago by
Pedro Fernandes10 wrote:
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 Cięncia Apartado 14 2781-901 OEIRAS PORTUGAL Tel +351 21 4407912 http://gtpb.igc.gulbenkian.pt
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