Changes between Version 3 and Version 4 of BigCompute


Ignore:
Timestamp:
Oct 28, 2010 11:03:22 AM (12 years ago)
Author:
Barbera van Schaik
Comment:

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  • BigCompute

    v3 v4  
    22
    33== Groningen cluster ==
    4 People: Morris, Freerk, more?
    54
     5'''People'''
     6UMCG: Morris, Freerk, more?
     7
     8'''Description'''
    69Description here about code template and automatic PBS script generation. Job submission/monitoring
    710
    8 == Running workflows on Dutch Life Science Grid ==
    9 People:
     11== Port applications to Dutch Life Science Grid ==
     12'''People'''
    1013* AMC: Antoine van Kampen, Barbera van Schaik, Silvia D Olabarriaga, Mark Santcroos
    1114* Sara/BiGGrid: Tom Visser, more?
    1215
     16'''Description'''
     17Software is going to be implemented as workflow components. The workflows will run on the Dutch life science grid.
     18
    1319* Information about the infrastructure: http://www.bioinformaticslaboratory.nl/twiki/bin/view/EBioScience/
    1420* Getting started: http://www.bioinformaticslaboratory.nl/twiki/bin/view/EBioScience/GettingStarted
     21
     22'''Implemented workflow components at AMC'''
     23
     24This list of workflow components are already available. We can expand it with Pindel and (parts of) the GATK pipeline.
     25
     26* Splitting of fastq files
     27* Building a BWA index on the genome sequence (base space and color space)
     28* BWA for shotgun reads (base space and color space) It is possible to do parameter sweeps. Output is in bam format
     29* Merge bam results
     30* Samtools pileup
     31* Varscan (pileup to snp, indel and cns)
     32* Bam2coverage creates a UCSC wiggle file to display the genome coverage (per 50kbp)
     33* Coverage-per-base determines the coverage for every base in the genome and it summarizes the results (coverage versus frequency)
     34* Annovar (currently working on the implementation). This is a pipeline to annotate variants (gene, dbsnp, hapmap, 1000g, conservation, etc)
     35
     36'''To be implemented'''
     37* BWA for paired end reads
     38* The components of the Groningen pipeline that not implemented as a workflow component yet
     39* Pindel
    1540
    1641== Alternatives ==