Difference between revisions of "Main Page"

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|* [[bcftools]]
 
|* [[bcftools]]
 
|* [[bedtools]]
 
|* [[bedtools]]
 +
|* [[bgenie]]
 
|* [[BLAST]]
 
|* [[BLAST]]
 
|* [[Blat]]
 
|* [[Blat]]
 +
|-
 
|* [[blast2go: b2g4pipe]]
 
|* [[blast2go: b2g4pipe]]
|-
 
 
|* [[bowtie]]
 
|* [[bowtie]]
 
|* [[bowtie2]]
 
|* [[bowtie2]]
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|* [[BUSCO]]
 
|* [[BUSCO]]
 
|* [[CAFE]]
 
|* [[CAFE]]
 +
|-
 
|* [[canu]]
 
|* [[canu]]
|-
 
 
|* [[cd-hit]]
 
|* [[cd-hit]]
 
|* [[cegma]]
 
|* [[cegma]]
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|* [[cramtools]]
 
|* [[cramtools]]
 
|* [[deeptools]]
 
|* [[deeptools]]
 +
|-
 
|* [[detonate]]
 
|* [[detonate]]
|-
 
 
|* [[diamond]]
 
|* [[diamond]]
 
|* [[ea-utils]]
 
|* [[ea-utils]]
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|* [[ETE]]
 
|* [[ETE]]
 
|* [[FASTQC and MultiQC]]
 
|* [[FASTQC and MultiQC]]
 +
|-
 
|* [[Archaeopteryx and Forester]]
 
|* [[Archaeopteryx and Forester]]
|-
 
 
|* [[GapFiller]]
 
|* [[GapFiller]]
 
|* [[GenomeTools]]
 
|* [[GenomeTools]]
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|* [[JBrowse]]
 
|* [[JBrowse]]
 
|* [[kallisto]]
 
|* [[kallisto]]
 +
|-
 
|* [[kentUtils]]
 
|* [[kentUtils]]
|-
 
 
|* [[last]]
 
|* [[last]]
 
|* [[lastz]]
 
|* [[lastz]]
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|* [[Mash]]
 
|* [[Mash]]
 
|* [[mega]]
 
|* [[mega]]
 +
|-
 
|* [[MUMmer]]
 
|* [[MUMmer]]
|-
 
 
|* [[NanoSim]]
 
|* [[NanoSim]]
 
|* [[OrthoFinder]]
 
|* [[OrthoFinder]]
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|* [[picard-tools]]
 
|* [[picard-tools]]
 
|* [[poRe]]
 
|* [[poRe]]
 +
|-
 
|* [[poretools]]
 
|* [[poretools]]
|-
 
 
|* [[prokka]]
 
|* [[prokka]]
 
|* [[pyrad]]
 
|* [[pyrad]]
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|* [[qualimap]]
 
|* [[qualimap]]
 
|* [[quast]]
 
|* [[quast]]
 +
|-
 
|* [[R]]
 
|* [[R]]
|-
 
 
|* [[RAxML]]
 
|* [[RAxML]]
 
|* [[Repeatmasker]]
 
|* [[Repeatmasker]]
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|* [[roary]]
 
|* [[roary]]
 
|* [[RSeQC]]
 
|* [[RSeQC]]
 +
|-
 
|* [[samtools]]
 
|* [[samtools]]
|-
 
 
|* [[Satsuma]]
 
|* [[Satsuma]]
 
|* [[sickle]]
 
|* [[sickle]]
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|* [[sra-tools]]
 
|* [[sra-tools]]
 
|* [[srst2]]
 
|* [[srst2]]
 +
|-
 
|* [[SSPACE]]
 
|* [[SSPACE]]
|-
 
 
|* [[stacks]]
 
|* [[stacks]]
 
|* [[Thor]]
 
|* [[Thor]]
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|* [[trimmomatic]]
 
|* [[trimmomatic]]
 
|* [[Trinity]]
 
|* [[Trinity]]
 +
|-
 
|* [[t-coffee]]
 
|* [[t-coffee]]
|-
 
 
|* [[velvet]]
 
|* [[velvet]]
 
|}
 
|}

Revision as of 16:51, 15 June 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 * ariba * assembly-stats * augustus * BamQC
* bamtools * bcftools * bedtools * bgenie * BLAST * Blat
* blast2go: b2g4pipe * bowtie * bowtie2 * bwa * BUSCO * CAFE
* canu * cd-hit * cegma * clustal * cramtools * deeptools
* detonate * diamond * ea-utils * ensembl * ETE * FASTQC and MultiQC
* Archaeopteryx and Forester * GapFiller * GenomeTools * gubbins * JBrowse * kallisto
* kentUtils * last * lastz * macs2 * Mash * mega
* MUMmer * NanoSim * OrthoFinder * PGAP * picard-tools * poRe
* poretools * prokka * pyrad * python * qualimap * quast
* R * RAxML * Repeatmasker * rnammer * roary * RSeQC
* samtools * Satsuma * sickle * SPAdes * sra-tools * srst2
* SSPACE * stacks * Thor * Tophat * 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

hdi2u

The half-day linux course held on 20th April. Modified version of I2U4BGA.

RNAseq for DGE


Templates