Lens culinaris: CDC Redberry Genome Assembly v1.2
Overview
Assembly Genome Size |
~2.7 Gb
|
---|---|
Scaffold N50 value |
~54,000
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Scaffold N50 length |
14,872
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Methodology
Genus |
Lens
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Scientific Name |
Lens culinaris
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Data Source Version |
Sequencing 2015
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Data Source Name |
CDC Redberry ASM
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Data Source URI |
Abbreviation |
Lc1.2.RBY
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Program, Pipeline, Workflow or Method Name |
USASK BettLab short-read genome assembly workflow
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Program Version |
2016
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The initial de novo sequence assembly was carried out using SOAPdenovo2 with input data consisting of 162X coverage paired end (library sizes ranging from 170-800bp) and 66X coverage mate pair data (2-8KB insert sizes). Libraries were discarded which deviated from the expected insert/fragment size. The resulting contigs were further refined using GapCloser using the initial paired end data and scaffolded with BAMBUS using a variety of large mate-pair libraries (insert sizes 20, 25, 30, 35, 40KB). PBJelly software was used for gap-filling and scaffold extension using 13X PacBio SMRT data. These scaffolds were anchored into 7 pseudomolecules using six high-density genetic linkage maps, with the total assembled bases representing over half of the 4 Gb lentil genome.
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This is not the most recent Lens culinaris, CDC Redberry assembly. Please do not use this assembly for new research projects. It is here for archival and citation purposes.
The following may be used as a citation for this assembly version:
Ramsay L, Chan C, Sharpe AG, Cook DR, Penmetsa RV, Chang P, Coyne C, McGee R, Main D, Edwards D, Kaur S, Vandenberg A, Bett KE (2016) Lens culinaris CDC Redberry genome assembly v1.2. Retrieved from https://knowpulse.usask.ca/genome-assembly/Lc1.2.