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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