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RNA-seq

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RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases.
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Related Experiment Video

Updated: Jun 23, 2025

Targeted RNA Sequencing Assay to Characterize Gene Expression and Genomic Alterations

Targeted RNA Sequencing Assay to Characterize Gene Expression and Genomic Alterations

Published on: August 4, 2016

SeqKit2: A Swiss army knife for sequence and alignment processing.

Wei Shen¹, Botond Sipos², Liuyang Zhao¹

¹Department of Infectious Diseases, Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Institute for Viral Hepatitis The Second Affiliated Hospital of Chongqing Medical University Chongqing China.

|June 20, 2024

Summary

This summary is machine-generated.

SeqKit2 enhances sequence analysis with 38 subcommands for comprehensive, user-friendly processing of high-throughput sequencing data. This powerful tool offers improved performance and new features for both novice and expert bioinformaticians.

Keywords:

performance optimization real‐time analysis sequence processing usability user‐friendly

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Last Updated: Jun 23, 2025

Targeted RNA Sequencing Assay to Characterize Gene Expression and Genomic Alterations

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Published on: August 4, 2016

Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease

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3' End Sequencing Library Preparation with A-seq2

3' End Sequencing Library Preparation with A-seq2

Published on: October 10, 2017

Area of Science:

Bioinformatics
Computational Biology
Genomics

Background:

High-throughput sequencing generates vast datasets requiring efficient analysis tools.
Existing tools often lack comprehensive functionality or user-friendliness for diverse bioinformatics needs.

Purpose of the Study:

Introduce SeqKit2, an advanced iteration of the SeqKit sequence analysis tool.
Expand functionality, optimize performance, and enhance usability for sequence and alignment processing.

Main Methods:

SeqKit2 incorporates 19 new subcommands, totaling 38 across eight categories.
New features include amplicon processing, error-tolerant record parsing, and real-time analysis subcommands.
Performance benchmarks compare SeqKit2 against SeqKit, Bioawk, Seqtk, and SeqFu.

Main Results:

SeqKit2 demonstrates consistent performance improvements over its predecessor.
It maintains competitive runtimes compared to other leading bioinformatics tools.
Expanded functionality enhances capabilities for diverse sequence analysis tasks.

Conclusions:

SeqKit2 offers a comprehensive, user-friendly, and performant solution for sequence and alignment processing.
Its broad functionality makes it suitable for both ad hoc analyses and integration into larger bioinformatics pipelines.
Ongoing development driven by user feedback ensures SeqKit2 remains a valuable tool for bioinformaticians.