Difference between revisions of "Main Page"
| Line 27: | Line 27: | ||
* [[srst2]] | * [[srst2]] | ||
* [[stacks]] | * [[stacks]] | ||
| + | * [[trimmomatic]] | ||
* [[velvet]] | * [[velvet]] | ||
Revision as of 16:03, 29 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
- 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 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
