Assemblathon 2 is a genome assembly contest where participating teams attempted to assemble genomes for three vertebrate species using a mixture of next-generation sequencing data. In total, 43 assemblies were submitted for three species (15 for bird, 16 for fish, and 12 for snake). These assemblies were assessed using a wide variety of statistical approaches as well as using experimental data from Fosmid sequences and optical maps.

Additional details

Read the peer-reviewed publication(s):

Bradnam, K. R., Fass, J. N., Alexandrov, A., Baranay, P., Bechner, M., Birol, I., … Chikhi, R. (2013). Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species. GigaScience, 2(1). doi:10.1186/2047-217x-2-10 (PubMed: 23870653)

Related datasets:

doi:10.5524/100060 IsSupplementedBy doi:10.5524/100061
doi:10.5524/100060 IsSupplementedBy doi:10.5524/100062

Accessions (data generated as part of this study):

SRA: ERP002324
SRA: SRA026860
SRA: ERP002294





Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
ERS218597499168Boa constrictor constrictor Boa constrictor constrictor
ERS22288013146Melopsittacus undulatusbudgerigarMelopsittacus undulatus Cell type:blood
Sex:male
Common name:budgerigar
SRS140425106582Maylandia zebrazebra mbunaMaylandia zebra Sex:male
Tissue:muscle and heart
Common name:zebra mbuna fish
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Displaying 1-3 of 3 Sample(s).




File NameSample IDData TypeFile FormatSizeRelease Date 
ERS222880Sequence assemblyFASTA314.04 MB2013-06-21
ERS222880Sequence assemblyFASTA312.02 MB2013-06-21
ERS222880Sequence assemblyFASTA326.11 MB2013-06-21
ERS222880Sequence assemblyFASTA322.81 MB2013-06-21
ERS222880Sequence assemblyFASTA329.14 MB2013-06-21
ERS222880Sequence assemblyFASTA321.07 MB2013-06-21
ERS222880Sequence assemblyFASTA328.5 MB2013-06-21
ERS222880Sequence assemblyFASTA320.45 MB2013-06-21
ERS222880Sequence assemblyFASTA328.44 MB2013-06-21
ERS222880Sequence assemblyFASTA320.67 MB2013-06-21
Displaying 1-10 of 87 File(s).
Date Action
October 27, 2015 File snake_7C_scaffolds.fa.gz updated