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Data released on June 24, 2013

Assemblathon 2 assemblies.

Alexandrov, A; Baranay, P; Bechner, M; Birol, I; Boisvert, S; Bradnam, K, R; Chapman, J, A; Chapuis, G; Chikhi, R; Chitsaz, H; Chou, W; Corbeil, J; Del Fabbro, C; Docking, T, R; Durbin, R; Earl, D; Emrich, S; Fass, J, N; Fedotov, P; Fonseca, N, A; Ganapathy, G; Gibbs, R, A; Gnerre, S; Godzaridis, ; Goldstein, S; Haimel, M; Hall, G; Haussler, D; Hiatt, J, B; Ho, I; Howard, J, T; Hunt, M; Jackman, S, D; Jaffe, D, B; Jarvis, E, D; Jiang, H; Kazakov, S; Kersey, P, J; Kitzman, J, O; Knight, J, R; Koren, S; Lam, T; Lavenier, D; Laviolette, F; Li, Y; Li, Z; Liu, B; Liu, Y; Luo, R; MacCallum, I; MacManes, M, D; Maillet, N; Melnikov, S; Naquin, D; Ning, Z; Otto, T, D; Paten, B; Paulo, O, S; Phillippy, A, M; Pina-Martins, F; Place, M; Przybylski, D; Qin, X; Qu, C; Ribeiro, F, J; Richards, S; Rokhsar, D, S; Ruby, J; Scalabrin, S; Schatz, M, C; Schwartz, D, C; Sergushichev, A; Sharpe, T; Shaw, T, I; Shendure, J; Shi, Y; Simpson, J, T; Song, H; Tsarev, F; Vezzi, F; Vicedomini, R; Vieira, B, M; Wang, J; Worley, K, C; Yin, S; Yiu, S; Yuan, J; Zhang, G; Zhang, H; Zhou, S; Korf, I, F (2013): Assemblathon 2 assemblies. GigaScience Database. RIS BibTeX Text

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.

Contact Submitter

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 included in GigaDB):

SRA: ERP002324
SRA: SRA026860
SRA: ERP002294



Samples: Table Settings


Common Name
Scienfic Name
Sample Attributes
Taxonomic ID
Genbank Name

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

Files: (FTP site) Table Settings


File Description
Sample ID
Data Type
File Format
Release Date
Download Link
File Attributes

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).



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