Hyalella azteca

Overview

Hyalella azteca is a freshwater epibenthic amphipod of interest to ecotoxicology and evolutionary biology. It is the primary invertebrate crustacean used in the U.S. for sediment toxicity testing and have been the subject of recent gene expression studies in ecotoxicogenomics.

H. azteca is a species complex which has diverged in North America over the past 11 million years creating numerous ecotypes which are the subject of divergent and convergent evolutionary studies.

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

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Community contact:

Image Credit: Helen Poynton. Image license: CC-BY 4.0.
Organism Image
Feature Summary
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Contig N50
5445
Scaffold N50
987977
Number Of Genes
12906
Community Contact
Community Contact: 
Helen C. Poynton|helen.poynton@umb.edu
Image Credit
Helen Poynton. Image license: <a href="https://creativecommons.org/licenses/by/4.0/">CC-BY 4.0</a>.

Assembly Information

Analysis Name Whole genome assembly of Hyalella azteca
Software Baylor College of Medicine genome assembly pipeline (NA)
Source Hazt.scaffolds
Date performed 2014-10-07
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

Statistics

Assembly Metrics
Contig N50 5445
Scaffold N50 987977
GC Content 38.69
Manual Annotations