bowtie2

Fast and sensitive gapped read aligner for DNA sequences

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Fast and sensitive gapped read aligner

bowtie2bowtie2-buildbowtie2-inspect

align DNA reads to a reference genome$ bowtie2 -x reference_index -U reads.fastq -S output.sam

build an index from a reference sequence$ bowtie2-build reference.fasta reference_index

align paired-end sequencing reads to reference$ bowtie2 -x reference_index -1 reads_R1.fastq -2 reads_R2.fastq -S output.sam

inspect and check a bowtie2 index$ bowtie2-inspect reference_index

align reads with specific parameters and save bam format$ bowtie2 -x reference_index -U reads.fastq -S output.sam --local -p 4