1. install
mamba install bwa

2. build index
bwa index <path to reference genome file>

3. alignment with single-end reads
bwa mem <path to reference genome file> <path to reads file> > <path to output sam file>

4. alignment with paired-end reads
bwa mem <path to reference genome file> <path to read 1 file> <path to read 2 file> > <path to output sam file>

5. alignment with PacBio subreads
bwa mem -x pacbio <path to reference genome file> <path to reads file> > <path to output sam file>

6. alignment with Oxford Nanopore reads
bwa mem -x ont2d <path to reference genome file> <path to reads file> > <path to output sam file>