Difference between revisions of "Main Page"

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|* [[BamQC]]
 
|* [[BamQC]]
 
|-
 
|-
 +
|* [[bamtools]]
 
|* [[bcftools]]
 
|* [[bcftools]]
 
|* [[bedtools]]
 
|* [[bedtools]]
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|* [[Blat]]
 
|* [[Blat]]
 
|* [[blast2go: b2g4pipe]]
 
|* [[blast2go: b2g4pipe]]
 +
|-
 
|* [[bowtie]]
 
|* [[bowtie]]
|-
 
 
|* [[bowtie2]]
 
|* [[bowtie2]]
 
|* [[bwa]]
 
|* [[bwa]]
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|* [[CAFE]]
 
|* [[CAFE]]
 
|* [[canu]]
 
|* [[canu]]
 +
|-
 
|* [[cd-hit]]
 
|* [[cd-hit]]
|-
 
 
|* [[cegma]]
 
|* [[cegma]]
 
|* [[clustal]]
 
|* [[clustal]]
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|* [[detonate]]
 
|* [[detonate]]
 
|* [[diamond]]
 
|* [[diamond]]
 +
|-
 
|* [[ea-utils]]
 
|* [[ea-utils]]
|-
 
 
|* [[ensembl]]
 
|* [[ensembl]]
 
|* [[ETE]]
 
|* [[ETE]]
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|* [[Archaeopteryx and Forester]]
 
|* [[Archaeopteryx and Forester]]
 
|* [[GapFiller]]
 
|* [[GapFiller]]
 +
|-
 
|* [[GenomeTools]]
 
|* [[GenomeTools]]
|-
 
 
|* [[gubbins]]
 
|* [[gubbins]]
 
|* [[JBrowse]]
 
|* [[JBrowse]]
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|* [[last]]
 
|* [[last]]
 
|* [[lastz]]
 
|* [[lastz]]
 +
|-
 
|* [[macs2]]
 
|* [[macs2]]
|-
 
 
|* [[Mash]]
 
|* [[Mash]]
 
|* [[mega]]
 
|* [[mega]]
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|* [[NanoSim]]
 
|* [[NanoSim]]
 
|* [[OrthoFinder]]
 
|* [[OrthoFinder]]
 +
|-
 
|* [[PGAP]]
 
|* [[PGAP]]
|-
 
 
|* [[picard-tools]]
 
|* [[picard-tools]]
 
|* [[poRe]]
 
|* [[poRe]]
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|* [[prokka]]
 
|* [[prokka]]
 
|* [[pyrad]]
 
|* [[pyrad]]
 +
|-
 
|* [[python]]
 
|* [[python]]
|-
 
 
|* [[qualimap]]
 
|* [[qualimap]]
 
|* [[quast]]
 
|* [[quast]]
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|* [[RAxML]]
 
|* [[RAxML]]
 
|* [[Repeatmasker]]
 
|* [[Repeatmasker]]
 +
|-
 
|* [[rnammer]]
 
|* [[rnammer]]
|-
 
 
|* [[roary]]
 
|* [[roary]]
 
|* [[RSeQC]]
 
|* [[RSeQC]]
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|* [[Satsuma]]
 
|* [[Satsuma]]
 
|* [[sickle]]
 
|* [[sickle]]
 +
|-
 
|* [[SPAdes]]
 
|* [[SPAdes]]
|-
 
 
|* [[sra-tools]]
 
|* [[sra-tools]]
 
|* [[srst2]]
 
|* [[srst2]]
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|* [[stacks]]
 
|* [[stacks]]
 
|* [[Thor]]
 
|* [[Thor]]
 +
|-
 
|* [[Tophat]]
 
|* [[Tophat]]
|-
 
 
|* [[trimmomatic]]
 
|* [[trimmomatic]]
 
|* [[Trinity]]
 
|* [[Trinity]]

Revision as of 11:59, 12 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 * BLAST * Blat * blast2go: b2g4pipe
* bowtie * bowtie2 * bwa * BUSCO * CAFE * canu
* cd-hit * cegma * clustal * cramtools * detonate * diamond
* ea-utils * ensembl * ETE * FASTQC and MultiQC * Archaeopteryx and Forester * GapFiller
* GenomeTools * gubbins * JBrowse * kallisto * 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