Summary
Resource Type
Analysis
Name
Simple Sequence Repeats (SSR) prediction ( J. nigra)
Program, Pipeline, Workflow or Method Name
SSR prediction pipeline
Program Version
n/a
Algorithm
Organism
Data Source
Source Name
: J nigra assembly
Date Performed
Tuesday, January 15, 2019 - 20:10

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 17,205,517
Untrimmed Bases 3,475,514,434
Reconstructed Fragments 7,033,939
Reconstructed Fragments - Bases 1,191,496,671
Dinucleotide repeats with primers 11,859
Trinucleotide repeats with primers 753
Tetranucleotide repeats with primers 139

Download Files:

Properties
Analysis Type
tripal_ssr
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