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Related Experiment Video

Updated: Nov 30, 2025

Novel Sequence Discovery by Subtractive Genomics

Novel Sequence Discovery by Subtractive Genomics

Published on: January 25, 2019

Clover: a clustering-oriented de novo assembler for Illumina sequences.

Ming-Feng Hsieh¹, Chin Lung Lu¹, Chuan Yi Tang^2,3

¹Department of Computer Science, National Tsing Hua University, Hsinchu, 30013, Taiwan.

BMC Bioinformatics

|November 18, 2020

Summary

Clover, a novel de novo assembler, addresses Illumina sequencing errors using a k-mer clustering approach. It demonstrates superior assembly quality and competitive runtime, enhancing genomic research.

Keywords:

DNA sequencing De bruijn graph De novo genome assembly

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Area of Science:

Genomics
Bioinformatics
Computational Biology

Background:

Next-generation sequencing (NGS) has driven advancements in genomics, necessitating efficient de novo assembly tools.
De novo assembly methods, particularly those based on de Bruijn graphs, are effective for Illumina reads.
Sequencing errors from platforms like Illumina pose challenges for de novo assembly accuracy and downstream genomic analyses.

Purpose of the Study:

To develop a novel de novo assembler, Clover, designed to mitigate sequencing errors inherent in Illumina data.
To evaluate Clover's performance against existing de Bruijn graph, overlap-layout-consensus, and string graph assemblers.

Main Methods:

Developed Clover, a de Bruijn assembler employing a k-mer clustering strategy inspired by the overlap-layout-consensus paradigm.
Benchmarked Clover against ABySS, SOAPdenovo, SPAdes, Velvet, Bambus2, CABOG, MSR-CA, and SGA using datasets from Staphylococcus aureus, Rhodobacter sphaeroides, and human chromosome 14.

Main Results:

Clover achieved superior assembly quality, indicated by improved corrected N50 and E-size metrics.
Clover demonstrated competitive runtimes compared to most evaluated assemblers, with SOAPdenovo being an exception.
Clover was successfully applied in sequencing projects for bacterial genomes Acinetobacter baumannii TYTH-1 and Morganella morganii KT.

Conclusions:

Clover's clustering-based approach effectively integrates overlap-layout-consensus flexibility with de Bruijn graph efficiency for de novo assembly.
The developed assembler shows significant potential for improving the accuracy and reliability of genomic assembly.
Clover is available as open-source software.