Professor, Department of Animal Science, Faculty of Animal science and Food Technology, Agricultural Science and Natural Resources University of Khuzestan, Mollasani, Iran.
Abstract: (66 Views)
RNA sequencing (RNA-Seq) begins with aligning sequencing reads to a reference genome following quality control. Multiple alignment tools are available, but performance varies depending on data complexity and computational efficiency. This study compared the performance of two popular RNA-Seq aligners—TopHat2 and HISAT2—using four chicken embryo RNA-Seq datasets. Quality control was conducted using FastQC, and Trimmomatic was used for trimming and preprocessing. Results showed that HISAT2 successfully aligned 93.69% of the reads, outperforming TopHat2, which achieved 85.85%. Furthermore, HISAT2 assigned 88.68% of reads to specific genomic positions, compared to 79.35% for TopHat2. HISAT2 also demonstrated superior handling of multi-mapping and complex reads, in addition to offering faster processing and lower memory usage. These results confirm that HISAT2 provides more efficient and accurate alignment in transcriptomic studies, making it a preferred tool for RNA-Seq analysis.
Article number: 7
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