Difference between revisions of "Main Page"
| Line 35: | Line 35: | ||
* [[MUMmer]] | * [[MUMmer]] | ||
* [[OrthoFinder]] | * [[OrthoFinder]] | ||
| + | * [[quast]] | ||
* [[PGAP]] | * [[PGAP]] | ||
* [[prokka]] | * [[prokka]] | ||
Revision as of 13:32, 6 February 2017
Contents
Usage of Cluster
Documented Programs
- abacas
- augustus
- BamQC
- bedtools
- BLAST
- blast2go: b2g4pipe
- bowtie
- bowtie2
- bwa
- BUSCO
- CAFE
- cd-hit
- cegma
- clustal
- cramtools
- detonate
- diamond
- ensembl
- ETE
- FASTQC and MultiQC
- Archaeopteryx and Forester
- GapFiller
- gubbins
- JBrowse
- kallisto
- Mash
- mega
- MUMmer
- OrthoFinder
- quast
- PGAP
- prokka
- pyrad
- python
- RAxML
- Repeatmasker
- rnammer
- roary
- samtools
- SPAdes
- sra-tools
- srst2
- SSPACE
- stacks
- trimmomatic
- Trinity
- t-coffee
- 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)
Explanations
Pipelines
(Workflow with a specific end-goal)
- Trinity_Protocol
- STAR BEAST
- callSNPs.py
- Edgen RNAseq
- Miseq Prokaryote FASTQ analysis
- snpcallphylo
- Bottlenose dolphin population genomic analysis
Protocols
(Extensive workflows with different with several possible end goals)
Cluster Administration
- Hardware Issues
- Admin Tips
- RedHat
- Globus_gridftp
- Galaxy Setup
- Son of Gridengine
- Blas Libraries
- CMake
- Users and Groups
- node1 issues
- 6TB storage expansion
- Home directories max-out incident 28.11.2016
- Frontend Restart
- environment-modules
- H: drive on cluster
- Incident: Can't connect to BerkeleyDB
- Bioinformatics Wordpress Site
- Backups
- Python DRMAA
- SAN disconnect incident 10.01.2017
Courses
I2U4BGA
- Original schedule
- New schedule
- Actual schedule
- Course itself
- Directory Organization Exercise
- Glossary
- Key Bindings
- Cheatsheets
