SPAligner: alignment of long diverged molecular sequences to assembly graphs
Tatiana Dvorkina1, Dmitry Antipov2, Anton Korobeynikov2,3
1Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia. t.dvorkina@spbu.ru.
BMC Bioinformatics
|July 25, 2020
Summary
SPAligner efficiently aligns long nucleotide and amino acid sequences to genome assembly graphs. This novel tool aids in analyzing complex metagenomic data and advancing graph-based sequence alignment methods.
Area of Science:
- Bioinformatics
- Genomics
- Computational Biology
Background:
- Graph-based genome assembly representations are increasingly used for various applications.
- Current tools for aligning sequences to assembly graphs have limitations and cannot handle amino acid sequences.
- Amino acid sequence alignment to assembly graphs is crucial for applications like metagenomics.
Purpose of the Study:
- Introduce SPAligner, a new tool for aligning long nucleotide and amino acid sequences to assembly graphs.
- Evaluate SPAligner's efficiency in mapping sequencing reads to diverse assembly graphs.
- Demonstrate SPAligner's utility in identifying genes within complex metagenomic datasets.
Main Methods:
- Development of a novel alignment tool, SPAligner.
- Testing SPAligner on assembly graphs of varying complexity.
- Application of SPAligner for gene identification in metagenomic data.
Main Results:
- SPAligner demonstrates efficient alignment of long, diverged nucleotide sequences.
- SPAligner successfully aligns amino acid sequences to assembly graphs.
- The tool facilitates gene identification in complex metagenomic datasets.
Conclusions:
- SPAligner accelerates the development of graph-based sequence alignment solutions.
- SPAligner is integrated into the SPAdes tools library.
- The tool is publicly available on Github for broader use.
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