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Salmon-Easy: An alignment-free RNA-seq quantitative strategy based on partial genome indexing

Published: 08 August 2022 Publication History

Abstract

In recent years, transcriptome sequencing has been widely used in biological gene expression analysis, mutation analysis and many other aspects. The current second-generation high-throughput RNA sequencing raw data analysis methods have disadvantages such as high requirements for platform hardware, long time, and preference for analyzing species. Based on the comparison tool Salmon, we expanded its local genome indexing strategy and comparison method and established a second-generation RNA sequencing analysis process Salmon-easy. This method uses easily accessible genome sequence files and genome annotation files to effectively index part of the genome. In the process of processing the original sequencing data, the hardware occupancy is reduced, and the processing speed is increased. At the same time, comparing with the traditional method STAR based on alignment (Alignment-based) and Salmon based on CDS area index, it is found that Salmon-easy is more accurate and convenient. Therefore, the establishment of Salmon-easy provides a new idea for the analysis of the original data of second-generation RNA sequencing on low-configuration platforms.

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  1. Salmon-Easy: An alignment-free RNA-seq quantitative strategy based on partial genome indexing

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    ICBBT '22: Proceedings of the 14th International Conference on Bioinformatics and Biomedical Technology
    May 2022
    190 pages
    ISBN:9781450396387
    DOI:10.1145/3543377
    Permission to make digital or hard copies of all or part of this work for personal or classroom use is granted without fee provided that copies are not made or distributed for profit or commercial advantage and that copies bear this notice and the full citation on the first page. Copyrights for components of this work owned by others than ACM must be honored. Abstracting with credit is permitted. To copy otherwise, or republish, to post on servers or to redistribute to lists, requires prior specific permission and/or a fee. Request permissions from [email protected]

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    Published: 08 August 2022

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    1. RNA sequencing,Transcriptome quantification,Alignment-free,Partial genome indexing

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    • the National Natural Science Foundation of China

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