The study describing the Bowtie read alignment tool has been cited over 10,000 times since it first appeared in March 2009, according to Google Scholar. The Langmead Lab continues its hard work improving and maintaining this open source software, with a new version of Bowtie (1.2.1) having been released this week and two new versions of Bowtie 2 since the beginning of the year (now at 2.3.2). Recent improvements include parallel index building, native support for compressed inputs, greatly improved thread scaling, support for interleaved FASTQ, and many bug fixes and documentation improvements. We thank our funders for making this possible, especially the Intel Parallel Computing Program and NIH/NIGMS grant R01GM118568.