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CSAR-web: a web server of contig scaffolding using algebraic rearrangements
1Department of Computer Science, National Tsing Hua University, Hsinchu 30013, Taiwan.
Nucleic Acids Research
|May 8, 2018
Summary
CSAR-web is a novel tool for genome assembly scaffolding. It accurately orders and orients draft genome contigs using a reference genome, improving genome assembly quality.
Area of Science:
- Genomics
- Bioinformatics
Background:
- Genome assembly is a critical step in genomic research.
- Scaffolding draft genomes using reference genomes enhances contiguity and accuracy.
Purpose of the Study:
- To introduce CSAR-web, a web-based tool for efficient and accurate genome scaffolding.
- To provide a user-friendly platform for ordering and orienting draft genome contigs.
Main Methods:
- CSAR-web utilizes a rearrangement-based scaffolding algorithm.
- It identifies conserved genomic markers using either NUCmer (nucleotide comparison) or PROmer (amino acid comparison).
- Input includes target draft genome and reference genome in FASTA formats.
Main Results:
- CSAR-web successfully scaffolds contigs based on reference genomes.
- The tool provides visual (scalable dotplot) and tabular outputs for validation.
- It enables efficient and accurate ordering and orientation of draft genome contigs.
Conclusions:
- CSAR-web offers an effective solution for improving draft genome assembly quality.
- The web-based interface facilitates accessibility for researchers.
- This tool aids in the accurate reconstruction of complete or near-complete genomes.
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