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Novel Sequence Discovery by Subtractive Genomics
Published on: January 25, 2019
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Graph mining for next generation sequencing: leveraging the assembly graph for biological insights
Julia Warnke-Sommer1,2, Hesham Ali3,4
1College of Information Science and Technology, University of Nebraska Omaha, Omaha, NE, 68182, USA.
BMC Genomics
|May 8, 2016
Summary
A new hybrid graph model, Focus, aids metagenomics assembly and analysis. It reveals differences in antibiotic resistance genes between Crohn's disease patients and healthy individuals, outperforming existing assemblers.
Area of Science:
- Bioinformatics
- Genomics
- Computational Biology
Background:
- Metagenomics assembly of Next Generation Sequencing (NGS) data is challenging due to complex environmental samples.
- Current assemblers prioritize contig length and accuracy, often losing valuable overlap information.
- Assembly graphs capture rich genomic architecture, but novel modeling is needed.
Purpose of the Study:
- To develop a novel hybrid graph model for metagenomics data assembly and analysis.
- To utilize the Focus pipeline for creating and analyzing these hybrid graphs.
- To identify biologically relevant structures within the assembly graph for data mining.
Main Methods:
- Developed a novel hybrid graph model where nodes represent sequence regions at varying granularity.
- Applied the Focus assembly and analysis pipeline to metagenomics data from Crohn's disease patients and healthy individuals.
- Employed graph mining techniques to analyze hybrid graphs, focusing on antibiotic resistance and transposase genes.
Main Results:
- Hybrid graphs revealed associations between repetitive/mobile genetic elements and graph structure.
- Significant differences in the phylogenetic distribution of antibiotic resistance genes were found between healthy and Crohn's disease cohorts.
- Focus demonstrated excellent performance as a standalone assembly tool compared to Meta-velvet, Omega, and UD-IDBA.
Conclusions:
- Mining hybrid assembly graphs can uncover biological phenomena.
- Assembly graphs offer valuable data-mining support beyond their role in sequence assembly.
- The Focus pipeline provides a concise yet feature-rich view of metagenomics data.
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