Cronn Lab:Informatics: Difference between revisions
From OpenWetWare
Jump to navigationJump to search
No edit summary |
|||
Line 2: | Line 2: | ||
==Informatics Infrastructure== | ==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 - The original. Dual quad core 2.66 GHz Intel processors with 32 GB of RAM. | * 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 [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. | ||
Line 12: | Line 12: | ||
==Solexa Barcode Sorting== | ==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://brianknaus.com/software/srtoolbox/shortread.html Short read toolbox] - Includes barcode sorting script. | |||
==De Novo Assembly== | ==De Novo Assembly== | ||
Line 18: | Line 20: | ||
==Reference Based Assembly== | ==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]. | ||
Revision as of 14:16, 23 July 2010
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.
- 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.