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RNA-seq

RNA-seq

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.
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...

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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

iSeq: an integrated tool to fetch public sequencing data.

Haoyu Chao¹, Zhuojin Li², Dijun Chen²

¹Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou 310058, China.

Bioinformatics (Oxford, England)

|October 24, 2024

Summary

iSeq is a new command-line tool that simplifies retrieving metadata and next-generation sequencing (NGS) data from major public databases. This tool enhances the reanalysis of large-scale sequencing datasets.

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Area of Science:

Genomics
Bioinformatics
Computational Biology

Background:

High-throughput sequencing (next-generation sequencing, NGS) generates vast biological data.
Programmatic access to public NGS data and metadata from repositories like the Genome Sequence Archive (GSA) is limited.
Efficient data retrieval is crucial for addressing biological questions and reanalyzing existing datasets.

Purpose of the Study:

To develop a tool for streamlined programmatic access to public NGS data and metadata.
To facilitate data acquisition from multiple major sequencing databases.
To enhance the reanalysis of large-scale genomic datasets.

Main Methods:

Developed iSeq, a command-line interface tool.
Enabled simultaneous data retrieval from GSA, Sequence Read Archive (SRA), European Nucleotide Archive (ENA), and DNA Data Bank of Japan (DDBJ).
Implemented support for over 25 accession formats, Aspera downloads, parallel processing, and FASTQ file merging.

Main Results:

iSeq provides quick and straightforward retrieval of metadata and NGS data.
The tool supports diverse data sources and download protocols, simplifying data acquisition.
Features like parallel downloads and integrity verification enhance efficiency and reliability.

Conclusions:

iSeq significantly simplifies the process of accessing and managing public NGS data.
The tool empowers researchers by facilitating the reanalysis of large genomic datasets.
iSeq is freely available, promoting broader accessibility and use in the research community.