NGS Meeting on 18-12-2009
Discussions and updates
- Please follow links in the Agenda section to obtain the slides.
- A local Galaxy instance is running at Morris' group in UMCG.
- Bowtie supports color space reads now.
- Frans reported Maq and Bowtie as good alignment tools. Maq is already supported by the NBIC Life Science Grid Portal.
- Matt wrapped GAPSS as a Galaxy toolbox.
We reached the following agreements:
- Galaxy is agreed by the team as the common platform to share and integrate home-made tools and workflows. At the moment, NBIC research team is investigating into the possibilities and requirements to have a local instance of Galaxy. We will present some status update on the next NGS meeting.
- We will improve the Bio-Assist wiki page about NGS tools evaluation. We will also look into the possibilities to reach a broader audience, e.g. in WikiPedia and SEQanswers.
- Jan and Leon will work on the section about assembly.
- Frans and Leon will work on the section about alignment and SNP detection. Contributions from others are highly encouraged.
- A next meeting will be on 15-1-2010 before the regular Bio-Assist meeting. In that meeting, we will set up a further meeting/collaboration plan. A possibility is to rotate the meeting location among the participating groups.
The goal of this meeting is the following:
- introduce the opportunities in the NBIC NGS platform
- exchange information about (home made) software/methods
- seek for a common platform to share the workflows
- set up a further collaboration plan
Each responsible person will lead the discussion on one subject. Preparing slides are not mandatory but nice to have.
|9:00-9:10||Leon Mei||Introduction to the NBIC NGS Platform plan|
|9:10-9:30||Jan van Haarst||De novo assembly software|
|9:30-9:50||Frans Paul Ruzius||Benchmarking and comparison of mapping assembly software ( Report)|
|9:50-10:10||Matt Hestand||Generic pipelines and possibility on using one platform (e.g., Galaxy, Taverna) to share work flows/pipelines|
Surf meeting room
Hojel City Center, gebouw D (5th floor)
Graadt van Roggenweg 340
3531 AH Utrecht
9:00-10:15, 18 December 2009 (before the main BioAssist programmer meeting)
- Jan van Haarst (WUR)
- Matt Hestand (LUMC, Leiden)
- Victor de Jager (NBIC, Nijmegen)
- Leon Mei (NBIC, Rotterdam)
- Barbera van Schaik (AMC, Amsterdam)
- Marcel Willemsen (AMC, Amsterdam)
- Joris Lops (UMCG, Groningen)
- Morris Swertz (UMCG, Groningen)
- Frans Paul Ruzius (Hubrecht Institute, Utrecht)
- Wilfred van IJcken (EMC, Rotterdam)
- Stephan Nouwens (EMC, Rotterdam)
- Jurgen Piet (AMC, Amsterdam)
- Marc van Driel (NBIC)
- Rob Hooft (NBIC)
- Marco Roos (LUMC, Leiden)
- Machiel Jansen (SARA, Amsterdam)