Lens nigricans: ILWL 25 Genome Assembly v1.0
Overview
| Assembly Genome Size |
2.768 Gb
|
|---|---|
| Number Of Scaffolds |
1452
|
| Scaffold N50 length |
372 Mb
|
| Contig N50 Length |
4.45 Mb
|
| Number Of Genes |
39,758
|
Description
This Lens nigricans assembly was constructed with long-read Oxford nanopore data. Contigs were initially assigned their pseudomolecule position based on a reference-guided assembly with the Ler.1DRT assembly, and further validated and improved using HiC data in Juicebox. The finished assembly is 2.77 Gb arranged in 7 pseudo-molecules (96.9% of the genome sequence) and 1445 unplaced unitigs.
Methodology
| Genus |
Lens
|
|---|---|
| Scientific Name |
Lens nigricans
|
| Data Source Name |
ILWL 25
|
| Abbreviation |
Lni.1VIC
|
|---|---|
| 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 lack of a genetic map for L. nigricans, contigs were initially assigned pseudomolecule position based on a reference-guided assembly with L. ervoides Ler.1DRT assembly as the reference. This reference-guided assembly was done with the 'scaffold' command in RagTag. ALLHIC rescue was used to anchor the remaining contigs, and a final manual check was 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
Baker M, Ramsay L, Koh K, Bett KE (2022 Jun 23) Lens nigricans: ILWL 25 genome assembly (Lni.1VIC, version 1.0) [dataset]. University of Saskatchewan. Retrieved from https://knowpulse.usask.ca/genome-assembly/Lni.1VIC