A. arenosa sequencing project

New name

!Overview

[http://blogimages.seniorennet.be/waaroemni/143-5a476f599848fa4174d8216a2b011abb.jpg|right] The polyploid (4n) [Arabaidopsis (nee Cardaminopsis) arenosa|http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=38785&lvl=3&p=mapview&p=has_linkout&p=blast_url&p=genome_blast&lin=f&keep=1&srchmode=1&unlock] genome is being sequenced as part of the [Functional Genomics of Plant Polyploids|http://abc.polyploidy.org/index.php/Main_Page] NSF Plant Genome Project # 0077774. We are using a combination of paired-end and mate-paired Illumina reads to sequence to an approximate depth of 25x. Assemblies will be generated using Velvet and comparative analyses to the Arabidopsis lyrata and thaliana genomes will be performed.

!News

* June 20, 2009: Estimated 26x coverage sequence reads are now available.
!Data release
While we prepare our data for formal release into the NCBI Short Read Archive, we are making the raw reads available at this site.

!!Sample 1
17,794,664 76 bp paired end reads, average insert size 160 base pairs
# [Lane 1|./../data/FC30DCGAAXX/s_7_sequence.txt.gz] (862MB)
# [Lane 2|./../data/FC30DCGAAXX/s_8_sequence.txt.gz] (1.1GB)

!!Sample 2
29,028,087 51 bp paired end reads, average insert size 350 base pairs
# [Lane 1|./../data/FC30LV2AAXX/s_1_sequence.txt.gz] (710MB)
# [Lane 2|./../data/FC30LV2AAXX/s_2_sequence.txt.gz] (964MB)
# [Lane 3|./../data/FC30LV2AAXX/s_3_sequence.txt.gz] (1.1GB)

!Analysis

!Project Personnel
* Rob Martienssen (PI)
* Matt Vaughn (coPI, Assembly and informatics)
* Milos Tanurdzic (Library construction)
* Dick McCombie (Sequencing)
* Melissa de la Bastide (Sequencing informatics)
* Phil Tully (Intern)

!!Contact Information
If you have questions or comments about this sequencing project, please contact Rob Martienssen (martiens@cshl.edu) or Matt Vaughn (vaughn@cshl.edu) at Cold Spring Harbor Laboratory.
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