Difference between revisions of "Main Page"

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|* [[augustus]]
 
|* [[augustus]]
 
|* [[BamQC]]
 
|* [[BamQC]]
 +
|* [[bcftools]]
 
|-
 
|-
|* [[bcftools]]
 
 
|* [[bedtools]]
 
|* [[bedtools]]
 
|* [[BLAST]]
 
|* [[BLAST]]
 
|* [[blast2go: b2g4pipe]]
 
|* [[blast2go: b2g4pipe]]
 
|* [[bowtie]]
 
|* [[bowtie]]
|-
 
 
|* [[bowtie2]]
 
|* [[bowtie2]]
 
|* [[bwa]]
 
|* [[bwa]]
 +
|-
 
|* [[BUSCO]]
 
|* [[BUSCO]]
 
|* [[CAFE]]
 
|* [[CAFE]]
 
|* [[canu]]
 
|* [[canu]]
|-
 
 
|* [[cd-hit]]
 
|* [[cd-hit]]
 
|* [[cegma]]
 
|* [[cegma]]
 
|* [[clustal]]
 
|* [[clustal]]
 +
|-
 
|* [[cramtools]]
 
|* [[cramtools]]
 
|* [[detonate]]
 
|* [[detonate]]
|-
 
 
|* [[diamond]]
 
|* [[diamond]]
 
|* [[ensembl]]
 
|* [[ensembl]]
 
|* [[ETE]]
 
|* [[ETE]]
 
|* [[FASTQC and MultiQC]]
 
|* [[FASTQC and MultiQC]]
 +
|-
 
|* [[Archaeopteryx and Forester]]
 
|* [[Archaeopteryx and Forester]]
|-
 
 
|* [[GapFiller]]
 
|* [[GapFiller]]
 
|* [[GenomeTools]]
 
|* [[GenomeTools]]
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|* [[mega]]
 
|* [[mega]]
 
|* [[MUMmer]]
 
|* [[MUMmer]]
 +
|* [[NanoSim]]
 
|-
 
|-
|* [[NanoSim]]
 
 
|* [[OrthoFinder]]
 
|* [[OrthoFinder]]
 
|* [[quast]]
 
|* [[quast]]
 
|* [[PGAP]]
 
|* [[PGAP]]
 
|* [[picard-tools]]
 
|* [[picard-tools]]
|-
 
 
|* [[poRe]]
 
|* [[poRe]]
 
|* [[poretools]]
 
|* [[poretools]]
 +
|-
 
|* [[prokka]]
 
|* [[prokka]]
 
|* [[pyrad]]
 
|* [[pyrad]]
 
|* [[python]]
 
|* [[python]]
|-
 
 
|* [[R]]
 
|* [[R]]
 
|* [[RAxML]]
 
|* [[RAxML]]
 
|* [[Repeatmasker]]
 
|* [[Repeatmasker]]
 +
|-
 
|* [[rnammer]]
 
|* [[rnammer]]
 
|* [[roary]]
 
|* [[roary]]
|-
 
 
|* [[RSeQC]]
 
|* [[RSeQC]]
 
|* [[samtools]]
 
|* [[samtools]]
 
|* [[Satsuma]]
 
|* [[Satsuma]]
 
|* [[sickle]]
 
|* [[sickle]]
 +
|-
 
|* [[SPAdes]]
 
|* [[SPAdes]]
|-
 
 
|* [[sra-tools]]
 
|* [[sra-tools]]
 
|* [[srst2]]
 
|* [[srst2]]

Revision as of 17:46, 21 March 2017

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


Templates