1. Install the bowtie2
mamba install -c bioconda bowtie2 -y

2. Build an index using bowtie2
bowtie2-build --threads <number of alignment threads to launch> <path to genome fasta file> <path to Index filename prefix (minus trailing .X.bt2)>>

3. map reads to reference genome with bowtie2
#PE
bowtie2 -p <number of alignment threads to launch> -x <path to Index filename prefix (minus trailing .X.bt2)> -1 <path to read 1 file> -2 <path to read 2 file> -S <path to output sam file>

#SE
bowtie2 -p <number of alignment threads to launch> -x <path to Index filename prefix (minus trailing .X.bt2)> -U <path to read 1 file> -S <path to output sam file>