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Data released on April 26, 2014

Genomic data of the Golden-collared Manakin (Manacus vitellinus).

Gilbert, M, P; Jarvis, E, D; Li, B; Li, C; Schlinger, B; The Avian Genome Consortium, ; Wang, J; Zhang, G (2014): Genomic data of the Golden-collared Manakin (Manacus vitellinus). GigaScience Database. http://dx.doi.org/10.5524/101010 RIS BibTeX Text

The Golden-collared Manakin (Manacus vitellinus (Gould, 1843)) belongs to the Pipridae family of suboscine passseriform birds. It is commonly found in Colombia, Costa Rica and Panama.
These data have been produced as part of the G10K and Avian Phylogenomics Project. DNA was collected from a male obtained in Gamboa, Panama, with the sample obtained by Barney Schlinger of UCLA. We sequenced the genome to a depth of approximately 110X with short reads from a series of libraries with various insert sizes (170bp, 500bp, 800bp, 2kb, 5kb, 10kb and 20kb).
The assembled scaffolds of high quality sequences total 1.12Gb, with the contig and scaffold N50 values of 34kb and 2.5Mb respectively. We identified 15,285 protein-coding genes with a mean length of 18.8kb.

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Related manuscripts:

doi:10.1186/2047-217X-3-26
doi:10.1126/science.1251385
doi:10.1126/science.1253451

Related datasets:

doi:10.5524/101010 IsSupplementTo doi:10.5524/101000

Accessions (data included in GigaDB):

BioProject: PRJNA212872
SRA: SRP028393

Projects:



Genomic

http://gigadb.org/images/data/cropped/bird/manacus_vitellinus.png

Samples: Table Settings

Columns:

Common Name
Scienfic Name
Sample Attributes
Taxonomic ID
Genbank Name

Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
Golden-collared Manakin328815Golden-collared ManakinGolden-collared ManakinManacus vitellinus Source material identifiers:Erich Jarvis
Estimated genome size:unknown size
Funding source:BGI
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Displaying 1-1 of 1 Sample(s).

Files: (FTP site) Table Settings

Columns:

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

File NameSample IDFile TypeFile FormatSizeRelease Date 
Golden-collared ManakinCoding sequenceFASTA6.41 MB2014-04-26
Golden-collared ManakinSequence assemblyFASTA335.18 MB2014-04-26
Golden-collared ManakinAnnotationGFF1.6 MB2014-04-26
Golden-collared ManakinProtein sequenceFASTA4.17 MB2014-04-26
Golden-collared ManakinRepeat sequenceUNKNOWN9.53 MB2014-04-26
Displaying 1-5 of 5 File(s).

History:

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