README.md

Genome sequencing

For generating a Ribes nigrum genome, the cultivar Rosenthals Langtraubige was used. DNA was extracted and filtered for long fragments above 40 kbp in order to perform Oxford Nanopore (ONT) sequencing, PacBio sequencing and short read sequencing (Illumina).

Briefly, DNA was extracted, short fragments filtered out, DNA purity confirmed, and the libraries were prepared using the standard ONT protocol for the SQK-LSK112 kit. After DNA fragment repair and 3'-adenylation sequencing adapters were ligated to the DNA fragments, before a last purification step with AMPure XP beads. ONT sequencing was performed in-house, PacBio sequencing was performed by Genohub (Brigham Young University, Provo, UT, USA). Short read sequencing was performed by Genewiz.

Experimental workflow

Related repositories and files

This assay folder contains all information for the DNA isolation, library preparation and sequencing. Overall, the different steps performed for generating the R. nigrum genome were the following:

Plant growth

DNA isolation

Library preparation

Sequencing

Genome assembly

Genome analysis