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Next‐generation sequencing (NGS) technology has rapidly advanced and generated the massive data volumes. To align and map the NGS data, biologists often randomly select a number of aligners without concerning their suitable feature, high performance, and high accuracy as well as sequence variations and polymorphisms existing on reference genome. This study aims to systematically evaluate and compare the capability of multiple aligners for NGS data analysis. To explore this capability, we firstly performed alignment algorithms comparison and classification. We further used long‐read and short‐read datasets from both real‐life and in silico NGS data for comparative analysis and evaluation of these aligners focusing on three criteria, namely, application‐specific alignment feature, computational performance, and alignment accuracy. Our study demonstrated the overall evaluation and comparison of …