Changes between Version 3 and Version 4 of BigCompute

Timestamp:

Oct 28, 2010 11:03:22 AM (14 years ago)

Author:

Barbera van Schaik

Comment:

--

BigCompute

@@ -2 +2 @@
 
 == Groningen cluster ==
-People: Morris, Freerk, more?
 
+'''People'''
+UMCG: Morris, Freerk, more?
+
+'''Description'''
 Description here about code template and automatic PBS script generation. Job submission/monitoring
 
-== Running workflows on Dutch Life Science Grid ==
-People:
+== Port applications to Dutch Life Science Grid ==
+'''People'''
 * AMC: Antoine van Kampen, Barbera van Schaik, Silvia D Olabarriaga, Mark Santcroos
 * Sara/BiGGrid: Tom Visser, more?
 
+'''Description'''
+Software is going to be implemented as workflow components. The workflows will run on the Dutch life science grid.
+
 * Information about the infrastructure: http://www.bioinformaticslaboratory.nl/twiki/bin/view/EBioScience/
 * Getting started: http://www.bioinformaticslaboratory.nl/twiki/bin/view/EBioScience/GettingStarted
+
+'''Implemented workflow components at AMC'''
+
+This list of workflow components are already available. We can expand it with Pindel and (parts of) the GATK pipeline.
+
+* Splitting of fastq files
+* Building a BWA index on the genome sequence (base space and color space)
+* BWA for shotgun reads (base space and color space) It is possible to do parameter sweeps. Output is in bam format
+* Merge bam results
+* Samtools pileup
+* Varscan (pileup to snp, indel and cns)
+* Bam2coverage creates a UCSC wiggle file to display the genome coverage (per 50kbp)
+* Coverage-per-base determines the coverage for every base in the genome and it summarizes the results (coverage versus frequency)
+* Annovar (currently working on the implementation). This is a pipeline to annotate variants (gene, dbsnp, hapmap, 1000g, conservation, etc)
+
+'''To be implemented'''
+* BWA for paired end reads
+* The components of the Groningen pipeline that not implemented as a workflow component yet
+* Pindel
 
 == Alternatives ==