Cronn Lab:Informatics

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(Solexa barcode sorting)
 
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==Solexa Barcode Sorting==
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==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 resources:
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* pine1 - The original. Dual quad core 2.66 GHz Intel processors with 32 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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* smokey - 20 TB RAID system.
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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==
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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==''De Novo'' Assembly==
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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.
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For ''de novo'' assembly of micro-reads we typically use [http://www.ebi.ac.uk/~zerbino/velvet/ velvet].
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*[http://brianknaus.com/software/srtoolbox/shortread.html Short read toolbox] - Includes barcode sorting script.
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==Reference Based Assembly==
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''--- 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.''
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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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==Pine2 Software==
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==De novo assembly==
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The lab group is getting a new server named 'pine2.' During the setup process our wonderful sysadmin will be involved with installing 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, he usually uses old versions and does not update them. If you're interested in a particular version please state it.
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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.
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==Reference based assembly==
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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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*R 2.1.0
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==Lists of software==
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**ape
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[[Short read toolbox]]
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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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*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
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Current revision

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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.

--- 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

Personal tools