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GABI

GABI (Genomic Analysis of Bacterial Isolates) is a Nextflow pipeline for the quality control, assembly and characterization of bacterial isolates from short or long "next generation" sequencing reads.

It is designed to be easily installed and used, and work on a wide range of hardware configurations.

Highlights

  • ready-to-use reports
  • automatic sample classification
  • automatic handling of reference databases
  • requires only Nextflow and a container/environment manager to run
  • easy deployment on a variety of configuartions through containerization

Citation

There is no publication for GABI yet - stay tuned! In the meantime, you can cite this repository should you use GABI in your research.

Acknowledgements

The GABI team gratefully acknowledges the use of design principles and code snippets from the nf-co.re project, whose fundamental contributions to the Nextflow community has greatly influenced our work on GABI.

In addition, GABI uses concepts and references developed for similar pipelines, specifically AQUAMIS and BakCharak.

Developer team

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

Marc Höppner, Landeslabor Schleswig-Holstein, LSH