Skip to content

Citation

If you use PIPA in your research, please cite:

Cerdeira, L. PIPA: Pipeline for Microbial Genomic Analysis. https://github.com/lcerdeira/Pipa

DOI: 10.5281/zenodo.19521044

DOI

Tool Citations

Please also cite the individual tools you use:

  • Prokka: Seemann T (2014) Prokka: rapid prokaryotic genome annotation. Bioinformatics. 30(14):2068-9.
  • SPAdes: Bankevich A et al. (2012) SPAdes: a new genome assembly algorithm. J Comput Biol. 19(5):455-77.
  • MLST: Seemann T, mlst, https://github.com/tseemann/mlst
  • Abricate: Seemann T, Abricate, https://github.com/tseemann/abricate
  • Flye: Kolmogorov M et al. (2019) Assembly of long, error-prone reads using repeat graphs. Nat Biotechnol. 37:540-546.
  • Canu: Koren S et al. (2017) Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Genome Res. 27(5):722-736.
  • Trim Galore: Krueger F, Trim Galore, https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/