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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 * ariba * assembly-stats * augustus * BamQC
* 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


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