Toward almost closed genomes with GapFiller
By Marten Boetzer, Walter Pirovano. Genome Biology, 2012
1,105 citations recorded by the source corpus.
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/.
Subfields: Molecular Biology, Plant Science
View Paper: https://www.semanticscholar.org/paper/cc9c8a81a5e2be0c8abdb39c905f5faaf621dd81
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In Molecular Biology
Citations in the corpus
- GetOrganelle: a fast and versatile toolkit for accurate de novo assembly of organelle genomes (2018, methodology): “…Genomics Workbench (https://www.qiagen-bioinformatics.com/) have been widely used to assemble the WGS data, after which the organelle genomic scaffolds/contigs were selected or filtered out using a reference genome for further concatenation [17] or post-assembly gap filling and closing [18, 19].”