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If you are on the lookout for a software utility that could assist you in aligning large sets of short DNA sequences to large genomes, Bowtie is at least worth a try.

What the scenarios in which Bowtie proves its relevance on the market have in common is the product’s responsiveness when handling sets of short reads where at least one valid alignment is included in most of the reads; when the reads are high-quality; as well as when there is a small number of alignments reported by reads.

The tool’s low memory footprint can be explained by the fact that it relies on a Burrows-Wheeler index to handle the genome, with the possibility of employing multiple processors at the same time in order to get enhanced alignment speed.

It must be noted that, under normal circumstances, the rate at which it is capable of aligning 35-base pair reads to the human genome is 25 million reads per hour, with lcolorspace, gapped, and paired-end alignment modes being supported.

Apart from that, you should know that SAM is among the file formats supported by Bowtie, which translates to the fact that the software utility can carry out tasks requiring collaborative efforts with the SAMtools consensus, indel callers, and SNP.

It is worth mentioning that Bowtie is a piece of software users can interact with via command lines, so some technical skills are required.