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 Biocomputinghigh-performance computing cluster. We currently own the following resources:

  • pine1 - The original. Dual quad core 2.66 GHz Intel processors with 32 GB of RAM.
  • pine2 - Dual quad core 2.13 GHz Intel processors with 96 GB of RAM.
  • smokey - 20 TB RAID system.

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.

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