In the inaugural edition of the open access journal Genes, scientists from CLC bio along with Michael M. Miyamoto from the University of Florida, published an article with corresponding free software for simulating de novo assemblies.
The overall quality of de novo sequencing projects depends on a wide range of parameters, including read lengths, single versus paired end reads, insert sizes, coverage, and sequencing technology. This assembly simulation software tool provides an unbiased guide to scientifically determine the ideal strategy for a given de novo sequence assembly project, including accounting for sequencing costs.
Professor Michael M. Miyamoto from the University of Florida, states: 'When you start a de novo sequencing project, you often basically don’t know what you’re looking for. By using this assembly simulator scientists can play around with the various parameters before they actually start spending money, time, and effort on sequencing. In essence, this tool can help scientists select the options that will provide them with the ideal scientific output.'
Chief scientific officer at CLC bio, Bjarne Knudsen, continues: 'At CLC bio we’re not only developing new versions of our software, but also recognise the long term scientific benefits from investing time and resources in theoretical bioinformatics. This assembly simulator is a product of these efforts and is being used for improving the upcoming versions of our own de novo assembler.'
The scientific paper is titled 'A computer simulator for assessing different challenges and strategies of de Novo sequence assembly.'