This repository contains files created when analyzing data in relation with the ARTIC protocol for SARS-CoV-2 using minION and Illumina novaSEQ approaches.
The aim of our experiments was to determine the optimal PCR annealing temperature for SARS-CoV-2 multiplex amplicon sequencing. We also compared the SARS-CoV-2 genomes obtained using Illumina and Oxford nanopore sequencers.
The file 'SARS-CoV-2-MiNion-2.ipynb' contains the scripts for data analysis of nanopore data. Data generated by Illumina novaSEQ sequencer was analyzed using a workflow in CLC genomics workbench v20.0.4 described here.
A manuscript containing results from the experimental study comparing both ARTIC-protocols is under preparation.
The required softwares are in the website hosting ARTIC bioinforatic protocol
- Guppy
- Samtools 1.10
- iVar
- CLC genomics workbench with plugins installed
NB: All analyses were performed on Ubuntu 18.04.5LTS operating system, memory 64GB, Intel Xeon(R) CPU v3 @ 1.6GHZ x 12, Graphics GeForce RTX 2080/PCIe/SSE2.