From b5037671d98765556ad3e4ceaf2bb9142c015790 Mon Sep 17 00:00:00 2001 From: Angela Kranz <a.kranz@fz-juelich.de> Date: Sun, 17 Nov 2024 17:01:02 +0000 Subject: [PATCH] Update README.md --- .../Ribes_nigrum_genome_sequencing/README.md | 19 +++++++++++++++++-- 1 file changed, 17 insertions(+), 2 deletions(-) diff --git a/assays/Ribes_nigrum_genome_sequencing/README.md b/assays/Ribes_nigrum_genome_sequencing/README.md index cf5daca..20f50ac 100644 --- a/assays/Ribes_nigrum_genome_sequencing/README.md +++ b/assays/Ribes_nigrum_genome_sequencing/README.md @@ -1,9 +1,24 @@ # Genome sequencing -For generating a *Ribes nigrum* genome assembly, 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 and PacBio 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). +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 + +The different steps performed for the R. nigrum genome were the following. The respective metadata and data can be found in the different folders: + +[DNA isolation](https://git.nfdi4plants.org/usadellab/ribes_nigrum_genome/-/tree/main/assays/Ribes_nigrum_genome_sequencing?ref_type=heads) + +[Library preparation](https://git.nfdi4plants.org/usadellab/ribes_nigrum_genome/-/tree/main/assays/Ribes_nigrum_genome_sequencing?ref_type=heads) + +[**Sequencing**](https://git.nfdi4plants.org/usadellab/ribes_nigrum_genome/-/tree/main/assays/Ribes_nigrum_genome_sequencing?ref_type=heads) **=> You are here!** + +[Genome assembly](https://git.nfdi4plants.org/usadellab/ribes_nigrum_genome/-/tree/main/runs/Ribes_nigrum_genome?ref_type=heads) + +Genome analysis + -- GitLab