Summary
Resource Type
Analysis
Name
Simple Sequence Repeats (SSR) prediction ( F. pennsylvanica)
Program, Pipeline, Workflow or Method Name
SSR prediction pipeline
Program Version
n/a
Algorithm
Organism
Data Source
Source Name
: F. pennsylvanica assembly
Date Performed
Saturday, May 25, 2019 - 08:53

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 36,367,468
Untrimmed Bases 7,346,228,536
Reconstructed Fragments 4,959,578
Reconstructed Fragments - Bases 751,621,434
Dinucleotide repeats with primers 2,161
Trinucleotide repeats with primers 435
Tetranucleotide repeats with primers 54

Download Files:

Properties
Analysis Type
tripal_ssr
Give Feedback!