Cronn Lab:Informatics

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==Informatics Infrastructure==
==Informatics Infrastructure==
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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 nodes:
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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.
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* smokey - The newest. Dual 12 core 2.66 GHz Intel processors with 96 GB of RAM.
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* pine2 - Dual quad core 2.13 GHz Intel processors with 96 GB of RAM.
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* pine2 - In the future... a growing pine forest.
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* 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.
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==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.
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*[http://brianknaus.com/software/srtoolbox/shortread.html Short read toolbox] - Includes barcode sorting script.
==De Novo Assembly==
==De Novo Assembly==
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==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].
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==Smokey Software==
 
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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.
 
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*R 2.1.0
 
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**ape
 
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**seqinr
 
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**RMySQL
 
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*Perl 5.10.1
 
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*BioPerl 1.6.0
 
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*Circos
 
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*Python 2.6.3
 
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*BioPython 1.52
 
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*MySQL
 
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*Emacs
 
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*Emacs Speaks Statistics
 
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*Seaview
 

Revision as of 16:16, 23 July 2010

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Contents

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.

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.

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