Summary
Resource Type
Analysis
Name
Simple Sequence Repeats (SSR) prediction (F. americana)
Program, Pipeline, Workflow or Method Name
SSR prediction pipeline
Program Version
n/a
Algorithm
Organism
Data Source
Source Name
: F. americana assembly
Date Performed
Sunday, November 17, 2019 - 23:29

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 (combination of two sequenced libraries):
Untrimmed Pairs 9,880,130
Untrimmed Bases 1,995,786,260
Reconstructed Fragments 1,912,469
Reconstructed Fragments - Bases 317,644,899
Dinucleotide repeats with primers 875
Trinucleotide repeats with primers 179
Tetranucleotide repeats with primers 25
Download Files:
Properties
Analysis Type
tripal_ssr
Biological Samples
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