bio-raum/gabi

Genomic Analysis of Bacterial Isolates, or GABI for short, is a bioinformatic workflow to assemble bacterial genomes, annotate genes, detect antimicrobial resistance genes, perform serotyping for select taxa as well assign MLST types. GABI currently supports both (Illumina) short reads and ONT/Pacbio long reads. Hybrid assembly approaches are supported for ONT|Pacbio + 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.

Developer team

GABI is developed and supported by the following people and organizations:

Marc Höppner, Landeslabor Schleswig-Holstein, LSH

Acknowledgements

We thank the developers of the AQUAMIS pipeline for making some of the building blocks on which GABI is based publically available - specifically the ConfindR database and validation data for Campylobacter spp. as well as the reference intervals for a broad range of bacteria to determine assembly status. In addition, we thank the nf-co.re community for developing the standards on which GABI is based.