Aligning Short Sequencing Reads with Bowtie

Abstract This unit shows how to use the Bowtie package to align short sequencing reads, such as those output by second‐generation sequencing instruments. It also includes protocols for building a genome index and calling consensus sequences from Bowtie alignments using SAMtools. Curr. Protoc. Bioinform . 32:11.7.1‐11.7.14. © 2010 by John Wiley & Sons, Inc.