Difference between revisions of "Main Page"
| Line 16: | Line 16: | ||
|* [[BamQC]] | |* [[BamQC]] | ||
|- | |- | ||
| + | |* [[bamtools]] | ||
|* [[bcftools]] | |* [[bcftools]] | ||
|* [[bedtools]] | |* [[bedtools]] | ||
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|* [[Blat]] | |* [[Blat]] | ||
|* [[blast2go: b2g4pipe]] | |* [[blast2go: b2g4pipe]] | ||
| + | |- | ||
|* [[bowtie]] | |* [[bowtie]] | ||
| − | |||
|* [[bowtie2]] | |* [[bowtie2]] | ||
|* [[bwa]] | |* [[bwa]] | ||
| Line 28: | Line 29: | ||
|* [[CAFE]] | |* [[CAFE]] | ||
|* [[canu]] | |* [[canu]] | ||
| + | |- | ||
|* [[cd-hit]] | |* [[cd-hit]] | ||
| − | |||
|* [[cegma]] | |* [[cegma]] | ||
|* [[clustal]] | |* [[clustal]] | ||
| Line 35: | Line 36: | ||
|* [[detonate]] | |* [[detonate]] | ||
|* [[diamond]] | |* [[diamond]] | ||
| + | |- | ||
|* [[ea-utils]] | |* [[ea-utils]] | ||
| − | |||
|* [[ensembl]] | |* [[ensembl]] | ||
|* [[ETE]] | |* [[ETE]] | ||
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|* [[Archaeopteryx and Forester]] | |* [[Archaeopteryx and Forester]] | ||
|* [[GapFiller]] | |* [[GapFiller]] | ||
| + | |- | ||
|* [[GenomeTools]] | |* [[GenomeTools]] | ||
| − | |||
|* [[gubbins]] | |* [[gubbins]] | ||
|* [[JBrowse]] | |* [[JBrowse]] | ||
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|* [[last]] | |* [[last]] | ||
|* [[lastz]] | |* [[lastz]] | ||
| + | |- | ||
|* [[macs2]] | |* [[macs2]] | ||
| − | |||
|* [[Mash]] | |* [[Mash]] | ||
|* [[mega]] | |* [[mega]] | ||
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|* [[NanoSim]] | |* [[NanoSim]] | ||
|* [[OrthoFinder]] | |* [[OrthoFinder]] | ||
| + | |- | ||
|* [[PGAP]] | |* [[PGAP]] | ||
| − | |||
|* [[picard-tools]] | |* [[picard-tools]] | ||
|* [[poRe]] | |* [[poRe]] | ||
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|* [[prokka]] | |* [[prokka]] | ||
|* [[pyrad]] | |* [[pyrad]] | ||
| + | |- | ||
|* [[python]] | |* [[python]] | ||
| − | |||
|* [[qualimap]] | |* [[qualimap]] | ||
|* [[quast]] | |* [[quast]] | ||
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|* [[RAxML]] | |* [[RAxML]] | ||
|* [[Repeatmasker]] | |* [[Repeatmasker]] | ||
| + | |- | ||
|* [[rnammer]] | |* [[rnammer]] | ||
| − | |||
|* [[roary]] | |* [[roary]] | ||
|* [[RSeQC]] | |* [[RSeQC]] | ||
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|* [[Satsuma]] | |* [[Satsuma]] | ||
|* [[sickle]] | |* [[sickle]] | ||
| + | |- | ||
|* [[SPAdes]] | |* [[SPAdes]] | ||
| − | |||
|* [[sra-tools]] | |* [[sra-tools]] | ||
|* [[srst2]] | |* [[srst2]] | ||
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|* [[stacks]] | |* [[stacks]] | ||
|* [[Thor]] | |* [[Thor]] | ||
| + | |- | ||
|* [[Tophat]] | |* [[Tophat]] | ||
| − | |||
|* [[trimmomatic]] | |* [[trimmomatic]] | ||
|* [[Trinity]] | |* [[Trinity]] | ||
Revision as of 12:59, 12 June 2017
Contents
[hide]Usage of Cluster
Documented Programs
The following can be seen as extra notes referring to these programs usage on the marvin cluster, with an emphais on example use-cases. Most, if not all, will have their own special websites, with more detailed manuals and further information.
| * abacas | * albacore | * ariba | * assembly-stats | * augustus | * BamQC |
| * bamtools | * bcftools | * bedtools | * BLAST | * Blat | * blast2go: b2g4pipe |
| * bowtie | * bowtie2 | * bwa | * BUSCO | * CAFE | * canu |
| * cd-hit | * cegma | * clustal | * cramtools | * detonate | * diamond |
| * ea-utils | * ensembl | * ETE | * FASTQC and MultiQC | * Archaeopteryx and Forester | * GapFiller |
| * GenomeTools | * gubbins | * JBrowse | * kallisto | * last | * lastz |
| * macs2 | * Mash | * mega | * MUMmer | * NanoSim | * OrthoFinder |
| * PGAP | * picard-tools | * poRe | * poretools | * prokka | * pyrad |
| * python | * qualimap | * quast | * R | * RAxML | * Repeatmasker |
| * rnammer | * roary | * RSeQC | * samtools | * Satsuma | * sickle |
| * SPAdes | * sra-tools | * srst2 | * SSPACE | * stacks | * Thor |
| * Tophat | * 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
- mapping.py
- Edgen RNAseq
- Miseq Prokaryote FASTQ analysis
- snpcallphylo
- Bottlenose dolphin population genomic analysis
- ChIP-Seq Top2 peak-calling
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
- emailing
- biotime machine
- 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
- Memory repair glitch 16.02.2017
- node9 network failure incident 16-20.03.2017
Courses
I2U4BGA
- Original schedule
- New schedule
- Actual schedule
- Course itself
- Biolinux Source course
- Directory Organization Exercise
- Glossary
- Key Bindings
- one-liners
- Cheatsheets
- Links
- pandoc modified manual
- Command Line Exercises
hdi2u
The half-day linux course held on 20th April. Modified version of I2U4BGA.
RNAseq for DGE
- Theoretical background
- Quality Control and Preprocessing
- Mapping to Reference
- Mapping Quality Exercise
- Key Aspects of using R
- Estimating Gene Count Exercise
- Differential Expression Exercise
- Functional Analysis Exercise
