Sequence alignment with bowtie2
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Aligning example reads

Align paired-end reads

To align paired-end reads included with Bowtie 2, stay in the same directory and run:

bowtie2 -x $REF -1 reads_1.fq -2 reads_2.fq -S eg2.sam

This aligns a set of paired-end reads to the reference genome, with results written to the file eg2.sam.

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