While this restriction may not be problematic for genomes with low rearrangement rates, some bacterial genomes are highly plastic with mobile regions that can be located in different genomic locations even in closely related species. Some assemblers, MIRA for example, can create a reference-based assembly, where the genome is scaffolded during the assembly process, and impose the complete genome structure of the reference on the assembly. Paired-end sequencing can greatly improve this by creating scaffolds, but if paired-end information is not available or has been exhausted, the similarity provided by a closely related reference genome can provide independent information to assist with scaffolding of the contigs. While read lengths are increasing, assembly and scaffolding of complete genome sequences often remains a challenge. Second generation sequencing remains the most cost-effective and readily available technique for complete genome sequencing. A web-based implementation is additionally provided to allow users to submit a reference genome and a set of contigs to be scaffolded. Scaffold_builder is written in Python and is available at. Moreover, we sequenced two genomes from Salmonella enterica serovar Typhimurium LT2 G455 and Salmonella enterica serovar Typhimurium SDT1291 and show that Scaffold_builder decreases the number of contig sequences by 53% while more than doubling their average length. Scaffold_builder was evaluated using simulated pyrosequencing reads of the bacterial genomes Escherichia coli 042, Lactobacillus salivarius UCC118 and Salmonella enterica subsp. when mate-pairs are not available or have already been exploited. This is independent of mate-pair information and can be used complementarily for genome assembly, e.g. The application Scaffold_builder was designed to generate scaffolds – super contigs of sequences joined by N-bases – based on the similarity to a closely related reference sequence. However, longer repeats such as ribosomal RNA operons cannot be accurately assembled using existing tools. Identical repeats shorter than the average read length can generally be assembled without issue. In particular, the abundance of repeat elements in genomes makes it difficult to assemble them into a single complete sequence. Genome sequencing has become routine, however genome assembly still remains a challenge despite the computational advances in the last decade.
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