Toward almost closed genomes with GapFiller

作者：Marten Boetzer, Walter Pirovano · 发表于：Genome biology · 年份：2012 · DOI：10.1186/gb-2012-13-6-r56 · 被引用次数：1210 · 研究领域：Chromosomal and Genetic Variations、Genomics and Phylogenetic Studies、CRISPR and Genetic Engineering

De novo assembly is a commonly used application of next-generation sequencing experiments. The ultimate goal is to puzzle millions of reads into one complete genome, although draft assemblies usually result in a number of gapped scaffold sequences. In this paper we propose an automated strategy, called GapFiller, to reliably close gaps within scaffolds using paired reads. The method shows good results on both bacterial and eukaryotic datasets, allowing only few errors. As a consequence, the amount of additional wetlab work needed to close a genome is drastically reduced. The software is available at http://www.baseclear.com/bioinformatics-tools/.