About¶
The team¶
- Alexander Thomas
- Thomas Battenfeld
- Simon Magin
- Johannes Koester
- Folker Meyer
Tools used in UnCoVar¶
| Stage | Step | Tool Illumina | Tool Nanopore | SARS-CoV-2 specific |
|---|---|---|---|---|
| Preprocessing | primer clipping | BAMClipper | NoTrAmp | no |
| quality clipping | fastp | fastp | no | |
| contamination removal | Kraken2 | Kraken2 | no | |
| denoising | - | Canu, Medaka | no | |
| Assembly | assembly | MEGAHIT, metaSPAdes | MEGAHIT, metaSPAdes | no |
| scaffolding | RaGOO | RaGOO | no | |
| Analysis | SNV calling | freeBayes, DELLY | Medaka variant, Longshot | no |
| SNV validation | Varlociraptor | Varlociraptor | no | |
| Lineage call | read based lineage assignment | Kallisto | Kallisto | no |
| lineage call | Pangolin | Pangolin | yes |
This project wouldn't be possible without several open source tools and libraries: