The files used for testing were obtained by downloading the following:
* NC_045512.2.fasta from https://www.ncbi.nlm.nih.gov/nuccore/NC_045512.2?report=fasta
* SRR11728627.fastq from https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR11728627
* SRR11728641.fastq from https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR11728641
* SRR11828387.fastq from https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR11828387
* SRR11828399.fastq from https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR11828399

And applying the following operations:

bowtie2-build NC_045512.2.fasta sars-cov-2
bowtie2 -x sars-cov-2 SRR11728627.fq -S SRR11728627.sam
bowtie2 -x sars-cov-2 SRR11728641.fq -S SRR11728641.sam
bowtie2 -x sars-cov-2 SRR11828387.fq -S SRR11828387.sam
bowtie2 -x sars-cov-2 SRR11828399.fq -S SRR11828399.sam
samtools view -b SRR11728627.sam > SRR11728627.bam
samtools view -b SRR11728641.sam > SRR11728641.bam
samtools view -b SRR11828387.sam > SRR11828387.bam
samtools view -b SRR11828399.sam > SRR11828399.bam