Whole Genome Assembly and Annotation of Quercus suber

BioSamples
Cross Reference
Publication
Summary
Publication
Ramos AM, Usié A, Barbosa P, Barros PM, Capote T, Chaves I, Simões F, Abreu I, Carrasquinho I, Faro C, Guimarães JB, Mendonça D, Nóbrega F, Rodrigues L, Saibo NJM, Varela MC, Egas C, Matos J, Miguel CM, Oliveira MM, Ricardo CP, Gonçalves S. The draft genome sequence of cork oak.. Scientific data. 2018 05 22; 5:180069.
Summary
Name
Whole Genome Assembly and Annotation of Quercus suber
Description

First draft genome of cork oak: de novo assembly strategy based on high-throughput sequence data, which generated a draft genome comprising 23,347 scaffolds and 953.3 Mb in size. A total of 79,752 genes and 83,814 transcripts were predicted, including 33,658 high-confidence genes. An InterPro signature assignment was detected for 69,218 transcripts, which represented 82.6% of the total. Validation studies demonstrated the genome assembly and annotation completeness and highlighted the usefulness of the draft genome for read mapping of high-throughput sequence data generated using different protocols.

Versions of software and tools used: Sickle; BWA v0.7.15; Jellyfish v2.2.6; GenomeScope; Ray v2.3.1; SGA v0.10.14; GARM v0.7.5; BEDtools v2.25.0; BESST v2.2.5; Gap Closer v1.12; Redundans v0.13a; Augustus v3.2.2; Maker v3.0.0; Star v2.5.2b; StringTie v1.3.1b; RepeatModeler; RepeatMasker;CEGMA v2.5; Blastp v2.6.0; NCBI-nr 11/Jan/2017; SwissProt 15/Mar/2017; eggNOG mapper v0.12.7; eggnog v4.5; InterProscan v5.22-61.0; BUSCO v1.22; GMAP v2017-06-20; LAST v914
Program, Pipeline, Workflow or Method Name
De novo assembly strategy based on high-throughput sequence data
Program Version
(in description)
Data Source
Source Name
: https://www.ncbi.nlm.nih.gov
Source Version
: GCF_002906115.1
Source URI
: https://www.ncbi.nlm.nih.gov/assembly/GCF_002906115.1