Citation
If you use Bakta in your research, please cite this paper:
Schwengers O., Jelonek L., Dieckmann M. A., Beyvers S., Blom J., Goesmann A. (2021). Bakta: rapid and standardized annotation of bacterial genomes via alignment-free sequence identification. Microbial Genomics, 7(11). https://doi.org/10.1099/mgen.0.000685
Bakta is standing on the shoulder of giants taking advantage of many great software tools and databases. If you find any of these useful for your research, please cite these primary sources, as well.
Tools
- tRNAscan-SE 2.0 https://doi.org/10.1093/nar/gkab688
- Aragorn https://doi.org/10.1093/nar/gkh152
- Infernal https://doi.org/10.1093/bioinformatics/btt509
- PilerCR https://doi.org/10.1186/1471-2105-8-18
- Pyrodigal https://doi.org/10.21105/joss.04296 Prodigal https://doi.org/10.1186/1471-2105-11-119
- Diamond https://doi.org/10.1038/s41592-021-01101-x
- BLAST+ https://doi.org/10.1186/1471-2105-10-421
- PyHMMER https://doi.org/10.21105/joss.04296 HMMER https://doi.org/10.1371/journal.pcbi.1002195
- AMRFinderPlus https://doi.org/10.1038/s41598-021-91456-0
- pyCirclize https://github.com/moshi4/pyCirclize
Databases
- Rfam: https://doi.org/10.1002/cpbi.51
- Mob-suite: https://doi.org/10.1099/mgen.0.000206
- DoriC: https://doi.org/10.1093/nar/gky1014
- AntiFam: https://doi.org/10.1093/database/bas003
- UniProt: https://doi.org/10.1093/nar/gky1049
- RefSeq: https://doi.org/10.1093/nar/gkx1068
- COG: https://doi.org/10.1093/bib/bbx117
- KEGG: https://doi.org/10.1093/bioinformatics/btz859
- PHROG: https://doi.org/10.1093/nargab/lqab067
- AMRFinder: https://doi.org/10.1128/AAC.00483-19
- ISFinder: https://doi.org/10.1093/nar/gkj014
- Pfam: https://doi.org/10.1093/nar/gky995
- VFDB: https://doi.org/10.1093/nar/gky1080