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i5k Workspace@NAL
U.S. Department of Agriculture

Whole genome assembly of Eurytemora affinis

Summary
Summary
Resource Type
Genome Assembly
Name
Whole genome assembly of Eurytemora affinis
Program, Pipeline, Workflow or Method Name
Baylor College of Medicine genome assembly pipeline
Program Version
NA
Data Source
Source Name
: SAMN02302763
Source URI
: https://www.ncbi.nlm.nih.gov/biosample/SAMN02302763/
Organism
E. affinis (Calanoid copepod)
Publication
Eyun SI, Soh HY, Posavi M, Munro JB, Hughes DST, Murali SC, Qu J, Dugan S, Lee SL, Chao H, Dinh H, Han Y, Doddapaneni H, Worley KC, Muzny DM, Park EO, Silva JC, Gibbs RA, Richards S, Lee CE. Evolutionary History of Chemosensory-Related Gene Families across the Arthropoda.. Molecular biology and evolution. 2017 08 01; 34(8):1838-1862.
Description

Sequence generation for assembly. For this project we are generating fairly high coverage in a number of different insert sized libraries. The assembly strategy is based around a seed allpaths assembly (the Broad Allpaths assembler) followed by seed assembly improvement using homegrown tools, Atlas-link and Atlas-GapFill, which can significantly improve the results.
Thus we generate sequence data to enable the Allpaths assembly. As of Nov 2011 this is: - 40X genome coverage in 180bp insert library (100bp reads forward and reverse); and 40X 3kb insert data. To enable better scaffolding and local gap filling we additionally generate 500bp, 1kb, 2kb, and 8kb insert sizes at > 20X coverage.

Source: Baylor College of Medicine i5K Project Summary
Cross Reference
Ag Data Commons