Difference between revisions of "Main Page"
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= Data Examples = | = Data Examples = | ||
| + | * [[Two Eel Scaffolds]] | ||
| − | * [[ | + | = Procedures = |
| + | (short sequence of tasks with a certain end, often, a simple script) | ||
| + | * [[Calculating coverage]] | ||
= Pipelines = | = Pipelines = | ||
| + | (Workflow with a specific end-goal) | ||
* [[Trinity_Protocol]] | * [[Trinity_Protocol]] | ||
* [[STAR BEAST]] | * [[STAR BEAST]] | ||
| Line 44: | Line 48: | ||
==Protocols== | ==Protocols== | ||
| + | (Extensive workflows with different with several possible end goals) | ||
[[Synthetic Long reads]] | [[Synthetic Long reads]] | ||
Revision as of 17:16, 28 June 2016
Contents
Usage of Cluster
Programs
- abacas
- BamQC
- BLAST
- blast2go: b2g4pipe
- bowtie2
- CAFE
- cd-hit
- diamond
- ensembl
- JBrowse
- kallisto
- multiqc
- MUMmer
- OrthoFinder
- PGAP
- prokka
- pyrad
- python
- samtools
- SPAdes
- sra-tools
- srst2
- stacks
- 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 end, often, a simple script)
Pipelines
(Workflow with a specific end-goal)
Protocols
(Extensive workflows with different with several possible end goals) Synthetic Long reads
