Lens culinaris: CDC Redberry Genome Assembly v2.0

Overview
L Ramsay, C Koh, D Konkin, D Cook, V Penmetsa, G Dongying, C Coyne, J Humann, S Kaur, J Dolezel, KE Bett (2019) Lens culinaris CDC Redberry Genome Assembly v2.0. Retrieved from https://knowpulse.usask.ca/genome-assembly/Lcu.2RBY
Date Released
February 2020
Data Source
Source Name
: CDC Redberry ASM
Statistics
Assembly Genome Size
3,690,413,039
Number Of Scaffolds
5,969
Scaffold N50 value
1,352,216
Scaffold N50 length
823
Assembly Details
Workflow/Pipeline Name
USASK BettLab long-read genome assembly workflow
Algorithm
smartdenovo
Program Version
n/a
Assembly of the contigs was done using smartdenovo with 34x coverage of PacBio SMRT and 20x coverage of Oxford nanopore reads. Contigs were polished with racon, using three rounds of long-read data mapped against the and one round of Illumina short read data (10x coverage). Five lanes of HiC data were generated, and a first pass of scaffolding and breaking of chimeric sequence was carried out using SALSA, followed by scaffolding using an optical map using Irys-scaffolding. Scaffolds were assigned to chomosome bins using a genetic map from the LR-01 RIL population exome capture data, and ordered and oriented within each bin using ALLHiC. Pseudomolecule assemblies were individually visualized and manual corrections to correct telomere tethering made using Juicebox.
Download

This genome is available in pre-release form. For access send a detailed request by email to Dr. Kirstin Bett (k.bett @ usask.ca).

Please contact Dr. Kirstin Bett for permission to publish an analysis using this genome assembly. Once permission is obtained, you can cite this assembly as

L Ramsay, C Koh, D Konkin, D Cook, V Penmetsa, G Dongying, C Coyne, J Humann, S Kaur, J Dolezel, KE Bett (2019) Lens culinaris CDC Redberry Genome Assembly v2.0. Retrieved from https://knowpulse.usask.ca/genome-assembly/Lcu.2RBY