Lens orientalis: BGE 016880 Genome Assembly 1.0
Overview
| Assembly Genome Size |
3.75 Gb
|
|---|---|
| Number Of Scaffolds |
696
|
| Scaffold N50 length |
504 Mb
|
| Contig N50 Length |
2.316 Mb
|
Description
This assembly of BGE 016880 (Lens orientalis) was constructed with long-read data (50x Oxford nanopore reads). There were 3 706 total contigs with the longest contig spanning 11.4 Mb. The contiguity of the assembly was further validated and improved using HiC data and a genetic map (LR-89; BGE 016880 x IG 72529 intraspecific RIL). The finished assembly is 3.75 Gb arranged in 7 pseudo-molecules and 689 unplaced unitigs (98.6% anchored).
Methodology
| Genus |
Lens
|
|---|---|
| Scientific Name |
Lens orientalis
|
| Data Source Version |
Sequencing 2021
|
| Data Source Name |
BGE 016880
|
| Abbreviation |
Lor.1WPS
|
|---|---|
| Program, Pipeline, Workflow or Method Name |
GenomeFocus long read genome assembly workflow for large and highly repetitive genomes
|
| Program Version |
Oct 2021
|
Analysis Method
Using the GenomeFocus workflow, long reads were assembled with smartdenovo and polished with racon. Due to the high degree of telomere tethering observed in Lens species, a genetic map (LR-89) was used to form the initial clusters for HiC data incorporation. ALLHiC is then used to order and orient contigs within each pseudomolecule cluster. Any corrections and a final manual check are made with Juicebox.
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Data Release
This genome is available in pre-release form. For access, send a detailed request by email to Dr. Kirstin Bett (k.bett(at)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
Ramsay L, Koh K, Bett KE (2022 Jun 23) Lens orientalis: BGE 016880 genome assembly (Lor.1WPS, version 1.0) [dataset]. University of Saskatchewan. Retrieved from https://knowpulse.usask.ca/genome-assembly/Lor.1WPS