Cronn Lab:Informatics: Difference between revisions
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==Informatics | ==Informatics infrastructure== | ||
Much of our computational needs are facilitated through dedicated nodes on Oregon State University's [http://corelabs.cgrb.oregonstate.edu/biocomputing Center for Genome Research and Biocomputing] high-performance computing cluster. We currently own the following | Much of our computational needs are facilitated through dedicated nodes on Oregon State University's [http://corelabs.cgrb.oregonstate.edu/biocomputing Center for Genome Research and Biocomputing]high-performance computing cluster. We currently own the following resources: | ||
* pine1 - | * pine1 - The original. Dual quad core 2.66 GHz Intel processors with 32 GB of RAM. | ||
* pine2 - | * 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 [http://www.redhat.com/ Enterprise Red Hat] Linux. | These systems are currently run through a 64 bit version of [http://www.redhat.com/ Enterprise Red Hat] Linux. | ||
==Solexa | ==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. | 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. | ||
== | *[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. | |||
==Reference | ''--- 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 [http://www.ebi.ac.uk/~zerbino/velvet/ velvet] for genomic DNA. We are now using the [http://trinityrnaseq.sourceforge.net/ Trinity] package for de novo assembly of RNA-seq data. | |||
==Reference based assembly== | |||
When we have a reasonable reference we use either [http://rga.cgrb.oregonstate.edu/ RGA] or [http://maq.sourceforge.net/ MAQ]. | When we have a reasonable reference we use either [http://rga.cgrb.oregonstate.edu/ RGA] or [http://maq.sourceforge.net/ MAQ]. | ||
== | ==Lists of software== | ||
[[Short read toolbox]] | |||
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.
