Assembly data

Note: most of these projects are older projects done when many of us were at the Center for Bioinformatics and Computational Biology (CBCB) at the University of Maryland. For newer assembly projects, see the Salzberg lab page, https://salzberg-lab.org/genome-projects.

GAGE and GAGE-B are evaluations of contiguity and accuracy of assemblies that are generated by some of most commonly used genome assemblers. GAGE-B (for assemblies of bacterial organisms) follows the standards set by GAGE.

This page contains links to many of the genomes we have assembled. The "Data download" link will take you to a page where you can get the assembly of the genome itself, along with genome annotation (in some cases).


Genome
Sequencing Center
Assembler
Downloads
Bos taurus (domestic cow) Baylor HGSC
Celera Assembler Data download
(See our paper in Genome Biology on the cow assembly) and UMD Overlapper
Trichomonas vaginalis TIGR Celera Assembler Assembly Archive
Brugia malayi TIGR Celera Assembler Data download
Caenorhabditis briggsae
Sanger Center
Celera Assembler Data download
Tetrahymena thermophila TIGR
Celera Assembler Data download
Trypanosoma cruzi TIGR Celera Assembler
Drosophila pseudoobscura Baylor College of Medicine
Human Genome Sequencing Center
Celera Assembler Data download
GenBank entry
Drosophila yakuba Washington University
Genome Sequencing Center
Celera Assembler Data download
Drosophila virilis Agencourt Bioscience Celera Assembler Data download
Assembly Archive


Drosophila (fruit fly) endosymbionts

Steven Salzberg and colleagues identified the sequence of the bacterial endosymbiont Wolbachia within the publicly available sequence data of several species of fruit fly. These results were reported in the open access journal Genome Biology:
Salzberg, S.L., Hotopp, J.C., Delcher, A.L., Pop, M., Smith, D.R., Eisen, M.B., Nelson, W.C. (2005) Serendipitous discovery of Wolbachia genomes in multiple Drosophila species. Genome Biol 6 (3):R23.

The assemblies of the endosymbiont genomes were performed with AMOScmp, and they can be obtained from:

Wolbachia endosymbiont of Drosophila annanasae - GenBank entry
Wolbachia endosymbiont of Drosophila simulans - GenBank entry
Wolbachia endosymbiont of Drosophila willistoni - (contigs) (traceIDs)


Bacterial Genomes

Genome
Sequencing Center
Assembler
Downloads
Bacillus Anthracis
Ames Ancestor
*
TIGR Celera Assembler Assembly Archive
Bacillus Anthracis
str. A1055
*
TIGR Celera Assembler Assembly Archive
Bacillus Anthracis
str. Australia 94
*
TIGR Celera Assembler Assembly Archive
Bacillus Anthracis
str. CNEVA-9066
*
TIGR Celera Assembler Assembly Archive
Bacillus Anthracis
str. Kruger B
*
TIGR Celera Assembler Assembly Archive
Bacillus Anthracis
str. Vollum
*
TIGR Celera Assembler Assembly Archive
Bacillus Anthracis
str. Western North America USA5153
*
TIGR Celera Assembler Assembly Archive
Borrelia afzelii TIGR Celera Assembler Assembly Archive
Burkholderia cepacia R1808
DOEJoint Genome Institute Celera Assembler Data download
Chloroflexus aurantiacus
DOE Joint Genome Institute Celera Assembler Data download
Methylobacillus flagellatus
DOE Joint Genome Institute Celera Assembler Data download
Pseudomonas aeruginosa PAb1 CBCB AMOScmp, Velvet Data download
Xanthomonasoryzae pathovar oryzicola TIGR Celera Assembler Data download
Xylella fastidiosa ANN1 DOE Joint Genome Institute Celera Assembler Data download
Xylella fastidiosa DIXON
DOE Joint Genome Institute Celera Assembler Data download
*Assemblies completed in partnership with TIGR

Plant Genomes

Genome
Sequencing Center
Assembler
Downloads
Pinus taeda UC Davis Celera Assembler Dendrome ftp