Simple Sequence Repeats (SSR) prediction (F. americana)
Summary
Download Files:
| 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 |
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| Date Performed | Saturday, April 1, 2023 - 10:40 |
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 |
