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 nodes:
- pine1 - The original. Dual quad core 2.66 GHz Intel processors with 32 GB of RAM.
- smokey - The newest. Dual 12 core 2.66 GHz Intel processors with 96 GB of RAM.
- pine2 - In the future... a growing pine forest.
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.
Smokey Software
Our lab group just installed a new server called 'smokey.' The sysadmin wunderkinds at OSU will get smokey on-line and instal 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, sysadmin 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
- Circos
- Python 2.6.3
- BioPython 1.52
- MySQL
- Emacs
- Emacs Speaks Statistics
- Seaview
