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i5k Workspace@NAL
U.S. Department of Agriculture

Agrilus planipennis

Overview

The emerald ash borer (EAB), Agrilus planipennis Fairmaire, is a relatively new invasive pest that has killed millions of North American ash (Fraxinus spp.) trees in both managed and natural forests of northeastern and Midwestern states since its discovery in 2002.

EAB has invaded 15 states (Illinois, Indiana, Iowa, Kentucky, Maryland, Michigan, Minnesota, Missouri, New York, Ohio, Pennsylvania, Tennessee, Virginia, West Virginia, and Wisconsin) and two Canadian provinces (Ontario and Quebec).

Economic cost of potential EAB damage to ash trees has been recently estimated to reach more than $10 billion with possible expansion of infestation to 25 States in the next 10 years.

Data were generated by the Baylor College of Medicine's i5k pilot project.

View the Baylor College of Medicine's data sharing policy.

Community contact:

Image Credit: Pennsylvania Department of Conservation and Natural Resources - Forestry , Bugwood.org. CCBY license. View Source.

Assembly Information

Analysis Name
Whole genome assembly of Agrilus planipennis
Software
Baylor College of Medicine genome assembly pipeline (NA)
Source
Agrilus planipennis genome assembly Aplan.scaffolds.50.fa
Date performed
2014-01-29
Materials & Methods

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

Assembly Metrics

Contig N50
6314
Scaffold N50
910924
GC Content
34.40

Data Files

NameLast modifiedSize
folder-parentParent Directory
folderBCM-After-Atlas2015-03-19 13:42
folderCurrent Genome Assembly2015-03-19 13:42