ScaffMatch

MOTIVATION: Next-generation high-throughput sequencing has become a state-of-the-art technique in genome assembly. Scaffolding is one of the main stages of the assembly pipeline. During this stage, contigs assembled from the paired-end reads are merged into bigger chains called scaffolds. Because of a high level of statistical noise, chimeric reads, and genome repeats the problem of scaffolding is a challenging task. Current scaffolding software packages widely vary in their quality and are highly dependent on the read data quality and genome complexity. There are no clear winners and multiple opportunities for further improvements of the tools still exist.
RESULTS: This article presents an efficient scaffolding algorithm ScaffMatch that is able to handle reads with both short (<600 bp) and long (>35 000 bp) insert sizes producing high-quality scaffolds. We evaluate our scaffolding tool with the F score and other metrics (N50, corrected N50) on eight datasets comparing it with the most available packages. Our experiments show that ScaffMatch is the tool of preference for the most datasets.
AVAILABILITY AND IMPLEMENTATION: The source code is available at http://alan.cs.gsu.edu/NGS/?q=content/scaffmatch.
CONTACT: mandric@cs.gsu.edu
SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

ScaffMatch: scaffolding algorithm based on maximum weight matching.

The software tool 'ScaffMatch' is a new efficient algorithm for scaffolding during genome assembly from high-throughput sequencing data. It can handle both short and long insert sizes, and has been shown to produce high-quality scaffolds in comparison to other available packages. 

ScaffMatch

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