I have a fastq file from Nanopore sequencing data that contains reads from both the UK and South Africa variants of SARS-CoV-2.
The variants are identified by three key mutations in the receptor-binding domain of Spike.
Aim Firstly, I want to determine the number of reads then belongs to UK and South Africa variant. Then, I will create a bam file from the fastq file using the SARS-CoV-2 reference genome.
- How do I determine the reads belonging to each variants?
- Are there any tools available to classify the reads based on the pre-defined mutation criteria?