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Rapid Assembly of Multi-Gene Constructs using Modular Golden Gate Cloning

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Published on: February 5, 2021

Multi-CAR: a tool of contig scaffolding using multiple references.

Kun-Tze Chen¹, Cheih-Jung Chen¹, Hsin-Ting Shen¹

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

BMC Bioinformatics

|February 4, 2017

Summary

A new tool, Multi-CAR, uses multiple reference genomes to accurately order and orient draft genome contigs. This improves genome assembly accuracy compared to single-reference methods, offering a more complete and precise genomic sequence.

Keywords:

Bioinformatics Contigs Multiple references Next-generation sequencing Scaffolding

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Area of Science:

Genomics
Bioinformatics

Background:

Draft genomes from short reads are fragmented into contigs with unknown order and orientation.
Single reference-based scaffolding tools can produce errors due to genomic rearrangements or distant phylogenetic relationships.
A single reference genome may be insufficient for accurate scaffolding.

Purpose of the Study:

To develop an improved scaffolding tool, Multi-CAR, that utilizes multiple reference genomes.
To enhance the accuracy of ordering and orienting contigs in draft genomes.

Main Methods:

Developed Multi-CAR, a heuristic method revising a single reference-based tool (CAR) to incorporate multiple references.
Multi-CAR does not require prior knowledge of phylogenetic relationships or paired-end read libraries.
Tested Multi-CAR on a real dataset of prokaryotic genomes and compared it with Ragout and MeDuSa.

Main Results:

Multi-CAR accurately orders and orients contigs using multiple reference genomes.
Experimental results demonstrate Multi-CAR outperforms Ragout and MeDuSa in sensitivity, precision, genome coverage, scaffold number, and scaffold N50 size.
Validated on a real dataset of prokaryotic genomes.

Conclusions:

Multi-CAR is an efficient tool for accurate draft genome scaffolding using multiple references.
The tool provides improved accuracy in ordering and orienting contigs.
A web server for Multi-CAR is available for public use.