Cronn Lab:Informatics: Difference between revisions
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*[http://nar.oxfordjournals.org/cgi/content/full/36/19/e122?maxtoshow=&hits=10&RESULTFORMAT=1&author1=cronn&andorexacttitle=and&andorexacttitleabs=and&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&resourcetype=HWCIT Nucl. Acids. Res.] - Article describing barcoding. | *[http://nar.oxfordjournals.org/cgi/content/full/36/19/e122?maxtoshow=&hits=10&RESULTFORMAT=1&author1=cronn&andorexacttitle=and&andorexacttitleabs=and&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&resourcetype=HWCIT Nucl. Acids. Res.] - Article describing barcoding. | ||
*[http://brianknaus.com/software/srtoolbox/shortread.html Short read toolbox] - Includes barcode sorting script. | *[http://brianknaus.com/software/srtoolbox/shortread.html Short read toolbox] - Includes barcode sorting 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== | ==De novo assembly== |
Latest revision as of 23:23, 12 September 2011
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.
--- 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.