Comparison of two software applications TopHat2 and HISAT2 used in chicken transcriptomic data analysisTechnical comparison of the capabilities of two software applications TopHat2 and HISAT2 in bioinformatics analysis of chicken transcriptomic data

Rostami, Sepideh; beigi nassiri, Mohammadtaghi; Nazari, Mahmoud; Cheraghizadeh, Mohsen

Volume 19, Issue 4 (4-2024) MGj 2024, 19(4): 317-323 | Back to browse issues page

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Rostami S, beigi nassiri M, Nazari M, Cheraghizadeh M. Comparison of two software applications TopHat2 and HISAT2 used in chicken transcriptomic data analysisTechnical comparison of the capabilities of two software applications TopHat2 and HISAT2 in bioinformatics analysis of chicken transcriptomic data. MGj 2024; 19 (4) : 7
URL: http://mg.genetics.ir/article-1-1876-en.html

Comparison of two software applications TopHat2 and HISAT2 used in chicken transcriptomic data analysisTechnical comparison of the capabilities of two software applications TopHat2 and HISAT2 in bioinformatics analysis of chicken transcriptomic data

Sepideh Rostami

, Mohammadtaghi Beigi nassiri ^*

, Mahmoud Nazari

, Mohsen Cheraghizadeh

Professor, Department of Animal Science, Faculty of Animal science and Food Technology, Agricultural Science and Natural Resources University of Khuzestan, Mollasani, Iran.

Abstract: (301 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

Keywords: read alignment, HISAT2, RNA-Seq, TopHat2.

Full-Text [PDF 616 kb] (41 Downloads)

Type of Study: Applicable | Subject: Subject 02
Received: 2024/12/10 | Accepted: 2025/03/18 | Published: 2025/07/5