Bowtie 2

Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp reads per hour. Bowtie indexes the genome with a Burrows-Wheeler index to keep its memory footprint small: typically about 2.2 GB for the human genome (2.9 GB for paired-end).



sudo apt-get install bowtie2

Input files

  • Genome reference in FASTA format;
  • Reads in FASTQ format.

Alignment (2 steps)

Step 1 – Index the reference fasta file

./bowtie2-build ref.fasta name_index

Step 2 – the alignment

./bowtie2 -X name_index -U reads.fastq -S aln.sam

Shell Script to run the Bowtie for all of your samples


./bowtie2-build gene.fasta gene  #index the reference sequence in fasta format

for file in *.fq  #run the alignment for all fastq files in the directory
file_name=`echo $arquivo | sed 's/\.fq//g'`
./bowtie2 -x gene -U $file -S $file_name.sam
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