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Usage of Cluster

Documented Programs

The following can be seen as extra notes referring to these programs usage on the marvin cluster, with an emphais on example use-cases. Most, if not all, will have their own special websites, with more detailed manuals and further information.

* abacas * albacore * assembly-stats * augustus * BamQC * bcftools
* bedtools * BLAST * blast2go: b2g4pipe * bowtie * bowtie2 * bwa
* BUSCO * CAFE * canu * cd-hit * cegma * clustal
* cramtools * detonate * diamond * ensembl * ETE * FASTQC and MultiQC
* Archaeopteryx and Forester * GapFiller * GenomeTools * gubbins * JBrowse * kallisto
* last * lastz * Mash * mega * MUMmer * NanoSim
* OrthoFinder * quast * PGAP * picard-tools * poRe * poretools
* prokka * pyrad * python * R * RAxML * Repeatmasker
* rnammer * roary * RSeQC * samtools * Satsuma * sickle
* SPAdes * sra-tools * srst2 * SSPACE * stacks * trimmomatic
* Trinity * t-coffee * velvet

Queue Manager Tips

A cluster is a shared resource with different users running different types of analyses. Nearly all clusters use a piece of software called a queue manager to fairly share out the resource. The queue manager on marvin is called Grid Engine, and it has several commands available, all beginning with q and with qsub being the most commonly used as it submits a command via a jobscript to be processed. Here are some tips:

Data Examples

Procedures

(short sequence of tasks with a certain short-term goal, often, a simple script)

Navigating genomic data websites

Explanations

Pipelines

(Workflow with a specific end-goal)

Protocols

(Extensive workflows with different with several possible end goals)

Cluster Administration

Courses

I2U4BGA

RNAseq for DGE

Templates