CIEVaD: a lightweight workflow collection for rapid and on demand deployment of end-to-end testing of genomic variant detection

Abstract

The identification of genomic variants has become a routine task in the thriving age of genome sequencing. Particularly small genomic variants of single or few nucleotides are routinely investigated for their impact on an organisms phenotype. Hence, precise and robust detection of the variants exact genomic location and change in nucleotide composition is vital in many biological applications. Although a plethora of methods exist for the many key steps of variant detection, thoroughly testing the detection process and evaluating its results is still a cumbersome procedure. In this work, we present a collection of trivial to apply and highly modifiable workflows to facilitate the generation of synthetic test data as well as to evaluate the accordance of a user-provided set of variants with the test data. AvailabilityThe workflows are implemented in Nextflow and are freely available and open-source at https://github.com/rki-mf1/cievad under the GPL-3.0 license.