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Related Experiment Video

Updated: Jun 22, 2026

Novel Sequence Discovery by Subtractive Genomics

Novel Sequence Discovery by Subtractive Genomics

Published on: January 25, 2019

De novo transcriptome assembly with ABySS.

Inanç Birol¹, Shaun D Jackman, Cydney B Nielsen

¹Genome Sciences Centre, Vancouver, BC V5Z 4S6, Canada. ibirol@bcgsc.ca

Bioinformatics (Oxford, England)

|June 17, 2009

Summary

This summary is machine-generated.

Whole transcriptome shotgun sequencing enables metabolic state studies. De novo assembly of transcriptomes, like follicular lymphoma tumor data, aids in discovering novel genetic events and transcripts.

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Area of Science:

Genomics
Bioinformatics
Transcriptomics

Background:

Whole transcriptome shotgun sequencing of non-normalized samples provides insights into organismal metabolic states.
Sequence coverage can infer gene expression levels, identify coding variations, and discover novel transcripts or isoforms.
De novo transcriptome assembly is crucial for identifying novel molecular events.

Purpose of the Study:

To perform de novo assembly of a follicular lymphoma tumor transcriptome.
To demonstrate the utility of whole transcriptome sequencing for discovering novel genetic information.

Main Methods:

Transcriptome sequencing using Illumina Genome Analyzer II platform with 36 bp single- and paired-end reads.
Assembly of approximately 194 million reads using the ABySS assembler.
Utilizing ABySS-Explorer for graph-based visualization and analysis.

Main Results:

Assembly of 66,921 contigs (≥100 bp) from follicular lymphoma tumor transcriptome.
Generated over 30 million base pairs of unique transcriptome sequence.
Maximum contig length of 10,951 bp, representing approximately 1% of the genome.

Conclusions:

De novo assembly of whole transcriptome shotgun sequencing data is effective for discovering novel transcripts and events.
The ABySS assembler is a powerful tool for large-scale transcriptome assembly.
This approach facilitates comprehensive analysis of tumor transcriptomes.