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i5k Workspace@NAL
U.S. Department of Agriculture

Whole genome assembly of Ephemera danica

Summary
Summary
Resource Type
Genome Assembly
Name
Whole genome assembly of Ephemera danica
Program, Pipeline, Workflow or Method Name
Baylor College of Medicine genome assembly pipeline
Program Version
NA
Data Source
Source Name
: SAMN02264621
Source URI
: https://www.ncbi.nlm.nih.gov/biosample/SAMN02264621/
Organism
E. danica (Mayfly)
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