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Related Concept Videos

Genome Annotation and Assembly

Genome Annotation and Assembly

The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.

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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Related Experiment Video

Updated: Jul 9, 2025

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

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

Published on: April 4, 2018

Seq2science: an end-to-end workflow for functional genomics analysis.

Maarten van der Sande¹, Siebren Frölich¹, Tilman Schäfers¹

¹Molecular Developmental Biology, Radboud University Nijmegen, Nijmegen, the Netherlands.

|November 29, 2023

Summary

This summary is machine-generated.

Seq2science is a versatile workflow for analyzing functional genomics data from public databases. It standardizes preprocessing, quality control, and analysis for diverse sequencing types across multiple species.

Keywords:

ATAC-seq ChIP-seq NGS RNA-seq Workflow

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Area of Science:

Genomics
Bioinformatics

Background:

Functional genomics sequencing databases offer vast resources for genome-scale analysis.
Reanalyzing and integrating public data with project-specific datasets is valuable but challenging due to standardization and reproducibility issues.
Current genomic experiment technologies enable analysis for numerous species.

Purpose of the Study:

To present Seq2science, a multi-purpose workflow designed to streamline the analysis of functional genomics sequencing data.
To facilitate data retrieval from major sequencing databases and genome assembly sources.
To provide standardized and reproducible analysis pipelines for various genomic experiments.

Main Methods:

Seq2science automates data downloading from NCBI SRA, EBI ENA, DDBJ, GSA, and ENCODE.
It retrieves genome assemblies from Ensembl, NCBI, and UCSC.
The workflow utilizes the Snakemake language for compatibility with diverse computing infrastructures and includes ATAC-, RNA-, and ChIP-seq analyses.

Main Results:

Seq2science covers preprocessing, quality control, visualization, and analysis steps.
It supports generic and advanced analyses like differential gene expression and motif analysis.
The workflow has been successfully tested on multiple species, demonstrating its versatility.

Conclusions:

Seq2science offers a standardized and reproducible solution for functional genomics data analysis.
It simplifies the integration of public and project-specific data, accelerating research.
The workflow enhances the accessibility and utility of large-scale genomic datasets.