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Lens culinaris: CDC Redberry Genome Assembly v1.2

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.
Overview
Date Released
May 2016
Data Source
Source Name
: CDC Redberry ASM
Source URI
: https://www.ncbi.nlm.nih.gov/biosample/5792392
Statistics
Assembly Genome Size
~2.7 Gb
Scaffold N50 value
~54,000
Scaffold N50 length
14,872
This version represents the final short read assembly of the Lens culinaris CDC Redberry genome which was distributed as a pre-release version. DNA was extracted from single seed descent plants and sequencing was carried out by next generation DNA sequencing with paired-end, mate-pair and long read libraries over a wide range of sizes and different technologies. This assembly consists of 7 chromosome and approximately 2.7 Gb of assembled sequence.
Assembly Details
Workflow/Pipeline Name
USASK BettLab short-read genome assembly workflow
Algorithm
SOAPdenovo2
Program Version
n/a
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.