Cronn Lab:Informatics

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.


 * Nucl. Acids. Res. - Article describing barcoding.
 * Short read toolbox - Includes barcode sorting 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.

Lists of software
Short read toolbox