Summary
Resource Type
Analysis
Name
Simple Sequence Repeats (SSR) prediction (G. triacanthos)
Program, Pipeline, Workflow or Method Name
SSR prediction pipeline
Program Version
n/a
Algorithm
Organism
Data Source
Source Name
: G. triacanthos assembly
Date Performed
Thursday, July 5, 2018 - 08:58

Publication: Staton M, Best T, Khodwekar S, Owusu S, Xu T, Xu Y, Jennings T, Cronn R, Arumuganathan AK, Coggeshall M, Gailing O. Preliminary Genomic Characterization of Ten Hardwood Tree Species from Multiplexed Low Coverage Whole Genome Sequencing. PloS one. 2015 Dec 23;10(12):e0145031.

In order to develop SSR resources for ten important North American hardwood tree species, we individually barcoded and multiplex sequenced DNA from ten hardwood forest tree species using short reads produced from an Illumina HiSeq. Raw reads can be downloaded from the NCBI short read archive, project SRP021923. Bioinformatic processing included trimming, assembly, SSR identification and primer design, processing details including scripts are available.

Statistics:

Untrimmed Pairs 15,327,293
Untrimmed Bases 3,096,113,186
Reconstructed Fragments 13,775,803
Reconstructed Fragments - Bases 2,147,108,245
Dinucleotide repeats with primers 4,084
Trinucleotide repeats with primers 544
Tetranucleotide repeats with primers 87

Download Files:

*The file of extended fragments is not available for download via web browser due to the very large size. In the meantime, please contact the site admin if you would like to download the file.

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