Difference between revisions of "Main Page"
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= Usage of Cluster= | = Usage of Cluster= | ||
[[Cluster Manual]] | [[Cluster Manual]] | ||
| + | [[Available Software]] | ||
| − | = Programs = | + | = Documented Programs = |
* [[abacas]] | * [[abacas]] | ||
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* [[sra-tools]] | * [[sra-tools]] | ||
* [[srst2]] | * [[srst2]] | ||
| + | * [[SSPACE]] | ||
* [[stacks]] | * [[stacks]] | ||
* [[trimmomatic]] | * [[trimmomatic]] | ||
Revision as of 13:35, 1 September 2016
Contents
Usage of Cluster
Cluster Manual Available Software
Documented Programs
- abacas
- augustus
- BamQC
- BLAST
- blast2go: b2g4pipe
- bowtie2
- BUSCO
- CAFE
- cd-hit
- cegma
- diamond
- ensembl
- FASTQC and MultiQC
- gubbins
- JBrowse
- kallisto
- multiqc
- MUMmer
- OrthoFinder
- PGAP
- prokka
- pyrad
- python
- rnammer
- RAxML
- samtools
- SPAdes
- sra-tools
- srst2
- SSPACE
- stacks
- trimmomatic
- 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)
File format expalanations
Pipelines
(Workflow with a specific end-goal)
Protocols
(Extensive workflows with different with several possible end goals) Synthetic Long reads
