Vigna unguiculata: IT97K-499-3 Genome Assembly v1.2
Overview
Assembly Genome Size |
519.4 Mb
|
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Number Of Scaffolds |
675
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Scaffold N50 value |
6
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Scaffold N50 length |
41.7 Mb
|
Number Of Genes |
31,948
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Methodology
Genus |
Vigna
|
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Scientific Name |
Vigna unguiculata
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Data Source Version |
Sequencing 2019
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Data Source Name |
IT97K-499-3
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Data Source URI |
Abbreviation |
vigun.IT97K-499-3
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Program, Pipeline, Workflow or Method Name |
Lonardi S et al., The Plant Journal 2019 06; 98(5):767-782
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Program Version |
2020
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Using Single Molecule Real-Time Sequencing (Pacific Biosciences) about six million long reads were generated for a total of 56.8Gbp (91x genome equivalent, assuming a genome size of 620Mb), with a read N50 of about 14.5Kbp. Eight draft assemblies were generated, six of which were produced with CANU v1.3 (using multiple parameter settings), one with Falcon v0.7.3 and one Abruijn v0.4. A custom assembly reconciliation algorithm merged the eight assemblies into one final stitched assembly, which was then polished via the PacBio Quiver pipeline in SMRT Portal. Two Bionano Genomics optical maps were used to assemble contigs into scaffolds. Finally, eleven pseudomolecules were produced using ALLMAPS by anchoring and orienting scaffolds to ten genetic maps containing a total of over forty-four thousand SNPs.
Download
LegFed DataStore | Access at CyVerse Data Commons |
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NCBI Bioproject | PRJNA381312 |
Original Source | Phytozome 13 |
This data is publicly available at the above locations. If you use this data in your research, please cite:
Lonardi S, Muñoz-Amatriaín M, Liang Q, Shu S, Wanamaker SI, Lo S, Tanskanen J, Schulman AH, Zhu T, Luo MC, Alhakami H, Ounit R, Hasan AM, Verdier J, Roberts PA, Santos JRP, Ndeve A, Doležel J, Vrána J, Hokin SA, Farmer AD, Cannon SB, Close TJ. The genome of cowpea (Vigna unguiculata [L.] Walp.).. The Plant journal : for cell and molecular biology. 2019 06; 98(5):767-782.