Genomic Analysis of Bacterial Isolates, or GABI for short, is a bioinformatic workflow to assemble bacterial genomes, annotate genes, detect antimicrobial resistance genes as well assign them to an (cg)MLST clustering schema. GABI supports both (Illumina) short reads and ONT/Pacbio long reads. Hybrid assembly approaches are supported for ONT/Illumina data sets and require for different read types to carry the same sample ID for grouping. Please see our documentation for detailed information.
If you are really impatient, check out our quickstart guide.
- What happens in this pipeline?
- Installation and configuration
- Running the pipeline
- Output
- Software
- Troubleshooting
- Developer guide
FooDMe2 is developed and supported by the following people and organizations:
Marc Höppner, Landeslabor Schleswig-Holstein, LSH