Currently whole-genome and targeted re-sequencing are the most popular NGS applications. In this application several tools are implemented to provide the best result for your re-sequencing project including read indexing and genome indexing algorithms, specialized assemblers for Roche 454, Illumina and ABI SOLiD platforms - including our proprietary color space assembler.
De novo assembly
De novo assembly is used in case of completely unknown sequences. Without a reference sequence, you can count on millions of overlapping reads from NGS machines. The most developed de novo algorithms available today are included in the application to guarantee the success of your de novo sequencing projects.
ChIP-Seq is used to analyze the protein interactions with the DNA. It combines chromatin immunoprecipitation (ChIP) with massively parallel DNA sequencing to identify the loci on the DNA that are associated with the protein of interest. The application can be used to determine the protein binding/histone modification sites from the distribution of NGS reads along the reference sequence with the help of complex algorithms that use specialized mathematical methods to identify significant read densities.
BLAST is the most frequently used tool to learn more about the similarity between the query sequence and the sequences stored in the selected database. BLAST has different variations according to the different sequence comparison methods. We have extended BLAST to enable comparison to any custom databases.
Hybrid de novo assembly
Most de novo sequencing projects combine the outputs from two or more different sequencing platforms (eg. long reads for a confident backbone and short reads for a high coverage). The aim of the hybrid de novo assembly application is to build up a genome or its parts by combining short/long and color coded/nucleotide coded reads. Unlike hybrid reference assembly, the read files produced by different sequencing technologies are assembled together as a joint set of mixed reads. Short reads can be single end, mate paired or paired end.
Hybrid reference assembly
A hybrid reference assembly application is used to assure the accurate alignment to the reference of the outputs from different sequencing platforms and to manage the joint result. Similarly to the standard reference assembly application, the alignment process involves the most suitable tools for the different datasets. The generated result files will be merged into a single BAM file.