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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: Oct 4, 2025

Leveraging CyVerse Resources for De Novo Comparative Transcriptomics of Underserved Non-model Organisms

Leveraging CyVerse Resources for De Novo Comparative Transcriptomics of Underserved Non-model Organisms

Published on: May 9, 2017

TransPi-a comprehensive TRanscriptome ANalysiS PIpeline for de novo transcriptome assembly.

Ramón E Rivera-Vicéns¹, Catalina A Garcia-Escudero^1,2, Nicola Conci¹

¹Department of Earth and Environmental Science, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, München, Germany.

Molecular Ecology Resources

|February 4, 2022

Summary

TransPi is a new pipeline for de novo transcriptome assembly, improving accuracy for nonmodel organisms. It enhances gene expression and phylogenetic studies by combining multiple assemblers for better results.

Keywords:

de novo Nextflow RNA-Seq annotation assembly nonmodel pipeline transcriptome

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Area of Science:

Bioinformatics
Computational Biology
Genomics

Background:

De novo transcriptome assembly from RNA sequencing (RNA-Seq) data is crucial for ecological and evolutionary studies, particularly in nonmodel organisms lacking genomic information.
Existing transcriptome assembly tools often require genome references or perform suboptimally with diverse datasets, necessitating multi-assembler approaches and automated workflows.
Current automated workflows are frequently limited to reference-based assemblies, restricting their application in nonmodel organisms.

Purpose of the Study:

To present TransPi, a comprehensive and user-friendly pipeline for de novo transcriptome assembly.
To enable thorough analysis of RNA-Seq data for nonmodel organisms with minimal user input.
To improve the accuracy and efficiency of transcriptome assembly compared to single-assembler methods.

Main Methods:

Developed TransPi, a comprehensive pipeline integrating multiple assemblers and a reduction step for de novo transcriptome assembly.
Assessed TransPi using various model organisms, k-mer sets, read lengths, and quantities.
Evaluated TransPi on transcriptome data from 49 diverse nonmodel organisms across different phyla.

Main Results:

TransPi achieved higher BUSCO (Benchmarking Universal Single-Copy Orthologs) completeness percentages compared to single-assembler approaches.
TransPi demonstrated a significant reduction in transcriptome duplication rates.
The pipeline is easily configurable and deployable via Conda, Docker, and Singularity.

Conclusions:

TransPi provides an effective solution for de novo transcriptome assembly, particularly for nonmodel organisms.
The pipeline enhances the reliability of downstream analyses such as differential gene expression and phylogenetics.
TransPi offers a reproducible, scalable, and user-friendly workflow for complex RNA-Seq data analysis.