Resource Type
Simple Sequence Repeats (SSR) prediction ( A. saccharum)
Program, Pipeline, Workflow or Method Name
SSR prediction pipeline
Program Version
Data Source
Source Name
: A. saccharum assembly
Date Performed
Wednesday, January 23, 2019 - 04:03

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 6,125,961
Untrimmed Bases 1,237,444,122
Reconstructed Fragments 675,883
Reconstructed Fragments - Bases 102,639,483
Dinucleotide repeats with primers 708
Trinucleotide repeats with primers 159
Tetranucleotide repeats with primers 24

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Analysis Type
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