Difference between revisions of "Main Page"
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* [[callSNPs.py]] | * [[callSNPs.py]] | ||
* [[Edgen RNAseq]] | * [[Edgen RNAseq]] | ||
| + | * [[Miseq Prokaryote FASTQ analysis]] | ||
=Protocols= | =Protocols= | ||
Revision as of 16:09, 18 July 2016
Contents
Usage of Cluster
Programs
- abacas
- BamQC
- BLAST
- blast2go: b2g4pipe
- bowtie2
- CAFE
- cd-hit
- diamond
- ensembl
- FASTQC and MultiQC
- 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
