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Related Experiment Video

Updated: Dec 28, 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

Compacta: a fast contig clustering tool for de novo assembled transcriptomes.

Fernando G Razo-Mendivil¹, Octavio Martínez², Corina Hayano-Kanashiro³

¹Departamento de Investigaciones Científicas y Tecnológicas de la Universidad de Sonora, Universidad de Sonora, Hermosillo, Mexico.

|February 13, 2020

Summary

Compacta is a new tool that efficiently selects representative transcriptomes from de novo assemblies. It helps researchers analyze gene expression in organisms with unknown genomes.

Keywords:

Corset Grouper RNA-Seq Transcriptomics de novo assembly

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Last Updated: Dec 28, 2025

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Novel Sequence Discovery by Subtractive Genomics

Novel Sequence Discovery by Subtractive Genomics

Published on: January 25, 2019

Area of Science:

Bioinformatics
Computational Biology
Genomics

Background:

RNA sequencing (RNA-Seq) is crucial for transcriptome exploration and differential gene expression analysis.
De novo assembly of RNA-Seq reads is necessary for organisms lacking a well-characterized genome.
Existing contig sets from de novo assembly often contain redundant transcripts, hindering downstream analysis.

Purpose of the Study:

To develop a computational tool, Compacta, for selecting a non-redundant set of contigs from de novo transcriptome assemblies.
To provide a method for improving the representation of transcriptomes for organisms with unknown genomes.

Main Methods:

Compacta utilizes a graph-based algorithm to cluster contigs based on shared reads.
Users can adjust parameters like minimum contig coverage and shared read proportion for dynamic transcriptome compression.
A pipeline for tailoring Compacta parameters to specific experimental goals is demonstrated.

Main Results:

Compacta demonstrated faster performance compared to state-of-the-art clustering algorithms.
The tool achieved competitive precision and recall ratios in transcriptome assembly analysis.
Evaluations were performed on de novo assemblies from Arabidopsis, mouse, and mango.

Conclusions:

Compacta is an efficient and adaptable algorithm for generating optimal contig sets.
The tool facilitates downstream transcriptome analyses by providing a refined set of representative contigs.