cd existing_repo
git remote add origin https://github.com/RIVM-bioinformatics/Submission-Assembler
git branch -M main
git push -uf origin main

This Snakemake pipeline was used to assemble data for our article 'Genomic surveillance of multidrug-resistant organisms based on long-read sequencing' submitted to Genome Medicine.

Will assemble longread data using six different assemblers. Canu, Flye, Miniasm and minipolish, Necat, Raven, Redbean, and Longcycler (Unicycler's long-read option)

#Step 1: Navigate to the directory where you want to clone the project

cd /path/to/your/directory

#Step 2: Clone the repository

git clone https://github.com/RIVM-bioinformatics/Submission-Assembler.git

#Step 3: Change into the project directory

cd your-repo

bash /path/to/your/directory/your-repo/start_longread_assembly.sh --longread /path/to/longread_data/ On default the output directory will be created inside current working directory + "assembly_YYMMDD_HHhMMmSSs" Optionally --output flag can be suplied.

Pipeline written by Fabian Landman and special thanks to Robert Verhagen for usage of cluster commands

This project is licensed under the MIT License - see the LICENSE file for details.

This pipeline has been uploaded for submission of our article only and shall not be further developed.