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bowtie2

Fast and sensitive gapped read aligner for DNA sequences

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About

Fast and sensitive gapped read aligner

Commands

bowtie2bowtie2-buildbowtie2-inspect

Examples

Build a Bowtie2 index from a reference genome FASTA file$ bowtie2-build reference.fa reference_index
Align paired-end reads to an indexed reference genome$ bowtie2 -x reference_index -1 reads_R1.fastq -2 reads_R2.fastq -S output.sam
Align single-end reads with sensitive settings and output BAM$ bowtie2 -x reference_index -U reads.fastq --sensitive -S output.sam | samtools view -b -o output.bam