Omnifluss

rki-mf1/omnifluss is a bioinformatics pipeline for the reconstruction of virus genomes. The word "omnifluss" is a neologism of the prefix omni ([ˈɔmni] - from Latin all or whole) and the word Fluss ([flʊs] - from German flow or flux).

Omnifluss takes raw sequencing data and performs operations such as quality filtering, primer clipping, taxanomic classification, alignment, variant calling, consensus assembly, and optionally reference selection. The specific algorithms and software selected for these operations primarily depend on two parameters: virus type and sequencing technology. Beside these two parameters many settings and subroutines can be finetuned. After a successful run omnifluss returns a consensus sequence, intermediate files, and an HTML report that includes statistics of the individual operations.

Technical prerequisites

For system requirements of omnifluss please see the Prerequisites page.

Analyse your data

For in depth guidance of how to use omnifluss with your data please see the individual virus pages.

---

Last update: October, 20th 2025