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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 * aspera * assembly-stats * augustus
* BamQC * bamtools * banjo * bcftools * bedtools * bgenie
* BLAST * Blat * blast2go: b2g4pipe * bowtie * bowtie2 * bwa
* BUSCO * CAFE * canu * cd-hit * cegma * clustal
* cramtools * conda * deeptools * detonate * diamond * ea-utils * ensembl
* ETE * FASTQC and MultiQC * Archaeopteryx and Forester * GapFiller * GenomeTools * gubbins
* JBrowse * kallisto * kentUtils * last * lastz * macs2
* Mash * mega * meryl * MUMmer * NanoSim * nseq
* OrthoFinder * PASA * perl * PGAP * picard-tools * poRe
* poretools * prokka * pyrad * python * qualimap * quast
* qiime2 * R * RAxML * Repeatmasker * Repeatmodeler * rnammer
* roary * RSeQC * samtools * Satsuma * sickle * SPAdes
* squid * sra-tools * srst2 * SSPACE * stacks * Thor
* Tophat * trimmomatic * Trinity * t-coffee * Unicycler * velvet
* ViennaRNA

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 specific end-goals)

Protocols

(Extensive workflows with different with several possible end goals)

Tech Reviews

Cluster Administration

Courses

I2U4BGA

hdi2u

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

RNAseq for DGE

Introduction to Unix 2017


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