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Welcome to the NGS-pipe wiki!

Here we describe the different aspects of NGS-pipe. NGS-Pipe provides analyses for large scale DNA and RNA sequencing experiments. The scope of pre-implemented functions spans the detection of germline variants, somatic single nucleotide variants (SNV) and insertion and deletion (InDel) identification, copy number event detection, and differential expression analyses. Further, it provides pre-configured workflows, such that the final mutational information as well as quality reports and all intermediate results can be generated quickly, also by inexperienced users. In addition, the pipeline can be used on a single computer or in a cluster environment where independent steps are executed in parallel. If one of the steps of the pipeline fails and produces incomplete or no results, the computation of all depending steps is halted and an error message is shown. However, after the issue is resolved the pipeline independently resumes the analyses at the appropriate point, eliminating the need to rerun the complete analysis or manual deletion of erroneous files.

For more information please read the corresponding wiki pages.