Cronn Lab:Informatics

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(De novo assembly)
Current revision (02:23, 13 September 2011) (view source)
(Solexa barcode sorting)
 
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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.
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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.''
==De novo assembly==
==De novo assembly==
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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 currently experimenting with the [http://trinityrnaseq.sourceforge.net/ Trinity] package for de novo assembly of RNA-seq data.
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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.
==Reference based assembly==
==Reference based assembly==

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