Bowtie2 output as BAM

Bowtie2 is a short read aligner that is optimized for aligning longer reads of lengths of 50 bp or greater. I’ve been playing around with it and was initially puzzled by the fact that it only outputs SAM formated alignments. Then I realized you can pipe the output straight into samtools which will do the compression to BAM for you.

$ bowtie2 \
-p 4 \
-x /genome/index \
-1 pair2.fastq \
-2 pair2.fastq \
-U unpaired.fastq \
--very-sensitive \
-X 1000 \
-I 200 \
| samtools view -bS - > output.bam