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susCovONT

Pipeline to generate consensus.fasta files and identify pangolin lineage and nextstrain clade of Sars-CoV-2 genomes from ONT sequencing.

This pipeline takes as input a folder with name <run_name> which contains the folders fast5_pass and fastq_pass and sequencing_summary*.txt from Sars-CoV-2 ONT sequencing together with a CSV-file which links barcode and sample name, and it outputs consensus.fasta files along with <run_name>_report.csv which includes pangolin lineage, nextstrain clade, mutations and QC.

Quick start

python susCovONT.py --input_dir /path/to/<run_name> --sample_names sample_names.csv

Where:

• --input_dir: Input directory <run_name> must contain fast5_pass and fastq_pass folders and sequencing_summary*.txt, with the <run_name> corresponding to your run (e.g. 20210213_1359_X5_FAO88697_5cf6e6f0)
• --sample_names: A CSV-file which connects barcodes with sample names, following the format:

barcode,sample_name
NB01,NEGCONTROL
NB02,E1234567_P1
NB03,V2345678_P1

Note: Basecalling and demultiplexing may also be performed if not already done on GridION/MinIT.

Quick install

All necessary tools can be installed with the ./scripts/install.sh script. You need to set the path of INSTALL_DIR, which is where the repositories will be installed (including this one), and you need to have conda and docker installed:

INSTALL_DIR="/home/marit/Programs/"  #Change to your install dir
cd $INSTALL_DIR
git clone https://github.com/marithetland/susCovONT  #Clone this repo
bash ./susCovONT/scripts/install.sh $INSTALL_DIR #Install all necessary tools

Please see the wiki for more information:

• What does the pipeline do?
• How to run
• Installation
• QC parameters and how to change these
• What does the output look like
• How to run the commands manually

And as an extra bonus:

• Setting up MinKNOW and RAMPART
• Further exploration using the Nexctlade Web Application

Note and thanks

Please note that this script was created for use at Stavanger University Hospital, you may need to change it (specifically the scripts/config.cfg file) for it to work in your environment.

This pipeline uses tools from the Artic network's nCoV-2019 novel coronavirus bioinformatics protocol. See also the QC and parameters page and further links here.

Many thanks to the artic, pangolin and nextclade developers for creating the protocols and pipelines!

Repo name

This pipeline was created for the analysis of Sars-CoV-2 data from Oxford Nanopore Technologies (ONT) sequencing at Stavanger University Hospital (SUH/SUS). Hence the name, susCovONT: SUS + Covid-19 + ONT.