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.

--- notice! --- As of summer 2011, we have been increasingly moving to Illumina's index sequencing method. Our experience to date from ~50 libraries has been very positive, and we are starting to explore novel indexes beyond the currently-available list of 24.

De novo assembly

For de novo assembly of micro-reads we typically use velvet for genomic DNA. We are now using the Trinity package for de novo assembly of RNA-seq data.

Reference based assembly

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

Lists of software

Short read toolbox