BaseTools: a wide range of bioinformatics solutions

..for Next Generation Sequencing (NGS) data analysis

BaseClear offers a wide range of bioinformatics solutions, primarily in the area of Next Generation Sequencing (NGS) data analysis. For this we mainly make a choice out of the most advanced software packages available on the market. However, especially in such a dynamic field as NGS, we frequently develop our own software solutions to fill in the gaps that are not covered by existing tools

We have started off this initiative with our stand-alone scaffolder called SSPACE. This tool has been published the high-impact journal Bioinformatics (2011, vol. 27(4), pag. 578-9). The basic version is freely available for download. From the large response in the field, and thousands of views on the SSPACE thread at the SEQanswers forum we were encouraged to further continue the development of SSPACE. The many (algorithmic) improvements made have resulted in the SSPACE Premium edition which includes our latest developments. Both SSPACE basic and SSPACE premium are maintained by our bioinformatics team and are regularly updated. SSPACE is already being frequently cited in high-impact journals such as Nature (Shinzato et al. (2011)) [link to: http://www.nature.com/nature/journal/v476/n7360/full/nature10249.html?WT.ec_id=NATURE-20110818.

Recently we have finished another valuable tool to finish genomes: GapFiller. This program automatically close gaps within scaffolds by taking advantage of paired-read data. GapFiller has now been submitted for publication. After acceptance of the manuscript we will make sure academic users can apply for a free license. Until that time a pre-release is available at the cost of 250,- euro (applicable to both academic and commercial users!).

Finally we have released a genome browser we call the BGB (BaseClear Genome Browser), This is a graphical tool to interactively visualize mutation data across multiple samples. The input is simply a reference genome, one or more coverage table(s) and SNP table(s). We offer a one-month trial license for free.

In principal our tools are not released for commercialization purposes, but in some cases we will ask you to either give a small contribution or get software for free in combination with a (sequencing) project. Please support us in creating innovative bioinformatics solutions for NGS analyses!

Questions?