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This wiki is meant as a repository for bioinformatical knowledge at the CEES. It is mainly run by Lex, but others are also very welcome to contribute.

  • If you want to be able to edit the wiki, let us know and we'll add you to the list of contributors.
  • If you add a page, please list it below! Tips for adding a page.


Mailing lists

  • cees-hpc: to be used for general information related to the area under /projects/cees, the able CPUs and the cod-nodes. Subscribe here.
  • cod-nodes: to be used to inform about the other cod-node users about CPUs and memory usage of the cod nodes, aka 'cod-node hugging' :-) USIT will also send emails to that list when discs on the nodes are full etc. Subscribe here.
  • cees-bioinf: to be used for general information regarding bioinformatics at CEES. Subscribe here.
  • Bioinformatics knowledge present at CEES


Use of the CEES hardware and Abel

User manual cod nodes

Abel use

Installing software and creating modules

Variant calling on Abel


Tips, tricks, useful links

Organising your computational work

Useful websites with Unix commands

Useful websites with Python tips and tricks

Useful websites with R tips and tricks

How-to's

PacBio smrtpipe command-line use

Submitting sequences to ENA

Quickly check the insert size distribution of a new sequencing library

Error correction of Illumina reads using merTrim from the Celera Assembler package

Assembly of Illumina paired end reads using Celera Assembler

File transfer through bioinf3.titan.uio.no