Bowtie2 Alignment

Build Index

# Build index from reference FASTA
bowtie2-build reference.fa reference_index

# With threads (faster)
bowtie2-build --threads 8 reference.fa reference_index

# Creates: reference_index.1.bt2, .2.bt2, .3.bt2, .4.bt2, .rev.1.bt2, .rev.2.bt2

Basic Alignment

# Paired-end reads
bowtie2 -p 8 -x reference_index -1 reads_1.fq.gz -2 reads_2.fq.gz -S aligned.sam