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
- 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
#!/bin/bash ./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 do file_name=`echo $arquivo | sed 's/\.fq//g'` ./bowtie2 -x gene -U $file -S $file_name.sam done