Open Access
American Research Journal of Computer Science and Information Technology
ISSN (Online): 2572-2921
DOI: 10.46568/arjcsit
Evaluation of Software of Next-Generation Sequencing in Mapping
Abstract
This study evaluates the performance of five next-generation sequencing (NGS) read mapping tools—BWA, Bowtie, Stampy,
Mosaik, and Agile—focusing on their behavior under varying conditions, including read errors, insertions, deletions, and
mutation rates. Reads from Illumina sequencing systems were simulated using dwgsim and further manipulated for
controlled testing. The evaluation assessed mapping precision, sensitivity, and computational efficiency using a 2.7 GB
reference genome to ensure compatibility across tools. Stampy demonstrated superior overall performance, particularly
with complex variations, but exhibited limitations in handling perfect reads with base quality “!” scores. Bowtie and
Mosaik performed well under specific conditions but struggled with paired reads and precision, respectively. Agile proved
incompatible with short reads, while BWA emerged as the fastest tool, albeit with precision issues at higher mutation
rates. Deletions posed the most significant challenge across all tools. These findings highlight critical trade-offs between
speed, accuracy, and adaptability in NGS read mapping tools, providing insights for their application in population
genomics and other domains.
