Comparative Evaluation of Short Read Alignment Tools for next Generation DNA Sequencing

The recent advancements in Next-generation sequencing technologies have resulted in an enormous amount of sequencing data with newer properties. An important step in all genomic analysis is aligning the reads to a reference genome. Numerous short read alignment tools are available to perform this time-consuming task. However, these tools have different trade-offs in terms of accuracy and speed. Hence, it is crucial to evaluate these tools based on various aspects to have a clear understanding of their performance. BWA MEM and Bowtie2 are selected to perform this evaluation mainly because they are designed to handle longer reads. The performance was evaluated using throughput and mapping percentage. The tools were put under several tests such as their ability to handle longer reads. The results indicate that one tool cannot outperform the other tool in all aspects. Bowtie2 achieved higher throughput in some cases while in other cases BWA MEM achieved higher throughput. However, BWA MEM had higher mapping percentage in most cases and handled longer reads more efficiently than Bowtie2.