Cronn Lab:Informatics

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Informatics Infrastructure

Much of our computational needs are facilitated through dedicated nodes on Oregon State University's Center for Genome Research and Biocomputing high-performance computing cluster. We currently own the following nodes:

  • pine1 - dual quad core 2.66 GHz Intel processors (a total of eight processors) with a total of 16 GB of RAM.
  • pine2 - coming online late 2009.
  • pine3 - still thinkin' about it.

These systems are currently run through a 64 bit version of Enterprise Red Hat Linux.

Solexa Barcode Sorting

Most of our Solexa runs include multiplex massively parallel sequencing (MMPS). Because these micro-reads include a sample-specific barcode (as well as the quality control 'T') a first step is to sort these reads by barcode and to remove the barcode. This is facilitated by a custom perl script.

De Novo Assembly

For de novo assembly of micro-reads we typically use velvet.

Reference Based Assembly

When we have a reasonable reference we use either RGA or MAQ.

Pine2 Software

The lab group is getting a new server named 'pine2.' During the setup process our wonderful sysadmin will be involved with installing software. In order to help get as much software as we would like on the system we're using this space as a list of softwares for him to install. In the interest of stability, he usually uses old versions and does not update them. If you're interested in a particular version please state it.

  • R 2.1.0
    • ape
    • seqinr
    • RMySQL
  • Perl 5.10.1
  • BioPerl 1.6.0
  • Python 2.6.3
  • BioPython 1.52
  • MySQL
  • Emacs
  • Emacs Speaks Statistics
  • Seaview