Using minor variant genomes and machine learning to study the genome biology of SARS-CoV-2 over time

AioMinor was implemented in Perl programming language, including a main script for nucletide and amino acid varation frequency in virus genome. It accepts bascalled fastq files derived from Nanopore amplicon sequencing, cleaned/trimmed Illumina amplicon/normal fastq files (single-end or paired-end) with a SARS-CoV-2/other virus genome. By default, AioMinor analyses SARS-CoV-2 based on an NCBI reference genome (NC_045512.2), but the user can also provide customized SARS-CoV-2 or other virus genome as a reference.