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# BaSSeT: Citations
## [nf-core](https://pubmed.ncbi.nlm.nih.gov/32055031/)
> Ewels PA, Peltzer A, Fillinger S, Patel H, Alneberg J, Wilm A, Garcia MU, Di Tommaso P, Nahnsen S. The nf-core framework for community-curated bioinformatics pipelines. Nat Biotechnol. 2020 Mar;38(3):276-278. doi: 10.1038/s41587-020-0439-x. PubMed PMID: 32055031.
## [Nextflow](https://pubmed.ncbi.nlm.nih.gov/28398311/)
> Di Tommaso P, Chatzou M, Floden EW, Barja PP, Palumbo E, Notredame C. Nextflow enables reproducible computational workflows. Nat Biotechnol. 2017 Apr 11;35(4):316-319. doi: 10.1038/nbt.3820. PubMed PMID: 28398311.
## Pipeline tools
- [Kaptive](https://github.com/klebgenomics/Kaptive)
> Lam, Margaret MC, Ryan R. Wick, Louise M. Judd, Kathryn E. Holt, and Kelly L. Wyres. "Kaptive 2.0: updated capsule and lipopolysaccharide locus typing for the Klebsiella pneumoniae species complex." Microbial genomics 8, no. 3 (2022): 000800.
> Stanton, Thomas David, Marit AK Hetland, Iren H. Löhr, Kathryn E. Holt, and Kelly L. Wyres. "Fast and accurate in silico antigen typing with Kaptive 3." Microbial genomics 11, no. 6 (2025): 001428.
> Wyres, Kelly L., Sarah M. Cahill, Kathryn E. Holt, Ruth M. Hall, and Johanna J. Kenyon. "Identification of Acinetobacter baumannii loci for capsular polysaccharide (KL) and lipooligosaccharide outer core (OCL) synthesis in genome assemblies using curated reference databases compatible with Kaptive." Microbial genomics 6, no. 3 (2019): e000339.
- [Kaptive database for _Vibrio parahaemolyticus_ O/K genotyping](https://github.com/aldertzomer/vibrio_parahaemolyticus_genomoserotyping)
> van der Graaf-Van Bloois, Linda, Hongyou Chen, Jaap A. Wagenaar, and Aldert L. Zomer. "Development of Kaptive databases for Vibrio parahaemolyticus O-and K-antigen genotyping." Microbial genomics 9, no. 5 (2023): 001007.
- [VicPred _Vibrio cholerae_ O-antigen database](https://doi.org/10.3389/fmicb.2021.691895)
> Lee, Imchang, Sung-Min Ha, Min-gyung Baek, Dong Wook Kim, Hana Yi, and Jongsik Chun. "VicPred: a Vibrio cholerae genotype prediction tool." Frontiers in Microbiology 12 (2021): 691895.
- [ECTyper](https://github.com/phac-nml/ecoli_serotyping)
> Bessonov, Kyrylo, Chad Laing, James Robertson, Irene Yong, Kim Ziebell, Victor PJ Gannon, Anil Nichani, Gitanjali Arya, John HE Nash, and Sara Christianson. "ECTyper: in silico Escherichia coli serotype and species prediction from raw and assembled whole-genome sequence data." Microbial genomics 7, no. 12 (2021): 000728.
- [HICap](https://github.com/scwatts/hicap)
> Watts, Stephen C., and Kathryn E. Holt. "hicap: in silico serotyping of the Haemophilus influenzae capsule locus." Journal of clinical microbiology 57, no. 6 (2019): 10-1128.
- [Kleborate](https://github.com/klebgenomics/Kleborate)
> Lam, Margaret MC, Ryan R. Wick, Stephen C. Watts, Louise T. Cerdeira, Kelly L. Wyres, and Kathryn E. Holt. "A genomic surveillance framework and genotyping tool for Klebsiella pneumoniae and its related species complex." Nature communications 12, no. 1 (2021): 4188.
- [el_gato](https://github.com/CDCgov/el_gato)
> Collins, Alan J., Dev Mashruwala, Vasanta Chivukula, Natalia A. Kozak-Muiznieks, Lavanya Rishishwar, Emily T. Norris, Melisa J. Willby, Jennafer AP Hamlin, and Will A. Overholt. "Epidemiology of Legionella: Genome-bAsed Typing (el_gato)-a new bioinformatic tool for identifying sequence-based types of Legionella pneumophila from whole genome sequencing data." bioRxiv (2026): 2026-03.
- [ABRicate](https://github.com/tseemann/abricate)
> Seemann T, *Abricate*, **Github** `https://github.com/tseemann/abricate`
> If you publish the results of Abricate please cite both the software _and_
the appropriate database you used with `--db`
> - [argannot](https://doi.org/10.1128/aac.01310-13)
> - [bacmet2](https://doi.org/10.1093/nar/gkt1252)
> - [card](https://doi.org/10.1093/nar/gkac920)
> - [ecoh](https://doi.org/10.1099/mgen.0.000064)
> - [ecoli_vf](https://github.com/phac-nml/ecoli_vf)
> - [megares](https://doi.org/10.1093/nar/gkac1047)
> - [ncbi](https://doi.org/10.1038/s41598-021-91456-0)
> - [plasmidfinder](https://doi.org/10.1128/AAC.02412-14)
> - [resfinder](https://doi.org/10.1093/jac/dkaa345)
> - [upec_expec_vf](https://github.com/FordeGenomics/ST167_Code/blob/main/UPEC-ExPEC_VF/UPEC_ExPEC_VF.tsv)
> - [vfdb](https://doi.org/10.1093/nar/gkae968)
> - [victors](https://doi.org/10.1093/nar/gky999)
- [ReporType databases](https://github.com/insapathogenomics/ReporType/tree/main/databases)
> Cruz, Helena, Miguel Pinheiro, and Vítor Borges. "ReporType: a flexible bioinformatics tool for targeted loci screening and typing of infectious agents." International Journal of Molecular Sciences 25, no. 6 (2024): 3172.
- [LisSero](https://github.com/MDU-PHL/LisSero)
> Kwong, J. C., Zhang, J., & Seeman, T. (2017) “LisSero: in silico serotyping of Listeria monocytogenes.” GitHub. https://github.com/MDU-PHL/LisSero
- [NGMASTER](https://github.com/MDU-PHL/ngmaster)
> Kwong, Jason C., Anders Gonçalves da Silva, Kristin Dyet, Deborah A. Williamson, Timothy P. Stinear, Benjamin P. Howden, and Torsten Seemann. "NGMASTER: in silico multi-antigen sequence typing for _Neisseria gonorrhoeae_." Microbial Genomics 2, no. 8 (2016): e000076.
- [meningotype](https://github.com/MDU-PHL/meningotype)
> Kwong Jason, Stroehlein Andreas, Anders Gonçalves da Silva & Torsten Seemann. “meningotype: in silico typing for _Neisseria meningitidis_.” GitHub. https://github.com/MDU-PHL/meningotype
- [Pasty](https://github.com/rpetit3/pasty)
> Petit, R. A. III “pasty: in silico serogrouping of _Pseudomonas aeruginosa_ isolates.” GitHub. https://github.com/rpetit3/pasty
- [SeqSero2](https://github.com/denglab/SeqSero2)
> Zhang, Shaokang, Hendrik C. Den Bakker, Shaoting Li, Jessica Chen, Blake A. Dinsmore, Charlotte Lane, A. C. Lauer, Patricia I. Fields, and Xiangyu Deng. "SeqSero2: rapid and improved _Salmonella_ serotype determination using whole-genome sequencing data." Applied and environmental microbiology 85, no. 23 (2019): e01746-19.
- [SISTR](https://github.com/phac-nml/sistr_cmd)
> Yoshida, Catherine E., Peter Kruczkiewicz, Chad R. Laing, Erika J. Lingohr, Victor PJ Gannon, John HE Nash, and Eduardo N. Taboada. "The Salmonella in silico typing resource (SISTR): an open web-accessible tool for rapidly typing and subtyping draft Salmonella genome assemblies." PloS one 11, no. 1 (2016): e0147101.
- [ShigaTyper](https://github.com/cfsan-biostatistics/shigatyper)
> Wu, Yun, Henry K. Lau, Teresa Lee, David K. Lau, and Justin Payne. "In silico serotyping based on whole-genome sequencing improves the accuracy of Shigella identification." Applied and environmental microbiology 85, no. 7 (2019): e00165-19.
- [ShigEiFinder](https://github.com/LanLab/ShigEiFinder)
> Zhang, Xiaomei, Michael Payne, Thanh Nguyen, Sandeep Kaur, and Ruiting Lan. "Cluster-specific gene markers enhance Shigella and enteroinvasive Escherichia coli in silico serotyping." Microbial genomics 7, no. 12 (2021): 000704.
- [AgrVATE](https://github.com/VishnuRaghuram94/AgrVATE)
> Raghuram, Vishnu, Ashley M. Alexander, Hui Qi Loo, Robert A. Petit III, Joanna B. Goldberg, and Timothy D. Read. "Species-wide phylogenomics of the Staphylococcus aureus agr operon revealed convergent evolution of frameshift mutations." Microbiology spectrum 10, no. 1 (2022): e01334-21.
- [sccmec](https://github.com/rpetit3/sccmec)
> Petit, R. A. III. “sccmec: a tool for typing SCCmec cassettes in assemblies.” GitHub. https://github.com/rpetit3/sccmec
> If you use `sccmec` in your research, please cite the following:
> * __[camlgmp](https://github.com/rpetit3/camlhmp)__
🐪Classification through yAML Heuristic Mapping Protocol 🐪
Petit III RA [camlhmp: Classification through yAML Heuristic Mapping Protocol](https://github.com/rpetit3/camlhmp) (GitHub)
> * __[BLAST](https://blast.ncbi.nlm.nih.gov/Blast.cgi)__
Basic Local Alignment Search Tool
*Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, Madden TL [BLAST+: architecture and applications](http://dx.doi.org/10.1186/1471-2105-10-421). BMC Bioinformatics 10, 421 (2009)*
- [spaTyper](https://github.com/HCGB-IGTP/spaTyper)
> Sánchez-Herrero, J. F., & Sull, M. J. “spaTyper: Staphylococcal protein A (spa) characterization pipeline.” Zenodo (2020). https://zenodo.org/badge/latestdoi/258175615
- [pbptyper](https://github.com/rpetit3/pbptyper)
> **PBP Typing Method**
_Li Y, Metcalf BJ, Chochua S, et al. [Penicillin-binding protein transpeptidase signatures for tracking and predicting β-lactam resistance levels in Streptococcus pneumoniae](https://journals.asm.org/doi/full/10.1128/mBio.00756-16) mBio 7(3):60 pii:e00756–16. (2016)_
> **pbptyper**
_Petit III RA [pbptyper: In silico Penicillin Binding Protein (PBP) typer for _Streptococcus pneumoniae_ assemblies](https://github.com/rpetit3/pbptyper) (GitHub)_
> **BLAST+**
_Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, Madden TL [BLAST+: architecture and applications.](http://dx.doi.org/10.1186/1471-2105-10-421) BMC Bioinformatics 10, 421 (2009)_
> **fastANI**
_Jain C, Rodriguez-R LM, Phillippy AM, Konstantinidis KT, Aluru S [High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries.](http://dx.doi.org/10.1038/s41467-018-07641-9) Nat. Commun. 9, 5114 (2018)_
- [SeroBA](https://github.com/sanger-pathogens/seroba)
> Epping, Lennard, Andries J. Van Tonder, Rebecca A. Gladstone, Global Pneumococcal Sequencing Consortium, Stephen D. Bentley, Andrew J. Page, and Jacqueline A. Keane. "SeroBA: rapid high-throughput serotyping of Streptococcus pneumoniae from whole genome sequence data." Microbial Genomics 4, no. 7 (2018): e000186.
> Lorenz, Oliver, Alannah C. King, Harry CH Hung, Feroze A. Ganaie, Anne L. Wyllie, Sam Manna, Catherine Satzke et al. "SeroBA (v2. 0) and SeroBAnk: a robust genome-based serotyping scheme and comprehensive atlas of capsular diversity in Streptococcus pneumoniae." Microbial Genomics 11, no. 10 (2025): 001483.
- [emmtyper](https://github.com/MDU-PHL/emmtyper)
> Andre Tan , Torsten Seemann, Kristy Horan, Jake Lacey, Himal Shrestha, Raquel Cooper & Anders Gonçalves da Silva. “emmtyper: emm Automatic Isolate Labeller.” GitHub. https://github.com/MDU-PHL/emmtyper
- [ARIBA](https://github.com/sanger-pathogens/ariba)
> Hunt, Martin, Alison E. Mather, Leonor Sánchez-Busó, Andrew J. Page, Julian Parkhill, Jacqueline A. Keane, and Simon R. Harris. "ARIBA: rapid antimicrobial resistance genotyping directly from sequencing reads." Microbial genomics 3, no. 10 (2017): e000131.
## Software packaging/containerisation tools
- [BioContainers](https://pubmed.ncbi.nlm.nih.gov/28379341/)
> da Veiga Leprevost F, Grüning B, Aflitos SA, Röst HL, Uszkoreit J, Barsnes H, Vaudel M, Moreno P, Gatto L, Weber J, Bai M, Jimenez RC, Sachsenberg T, Pfeuffer J, Alvarez RV, Griss J, Nesvizhskii AI, Perez-Riverol Y. BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics. 2017 Aug 15;33(16):2580-2582. doi: 10.1093/bioinformatics/btx192. PubMed PMID: 28379341; PubMed Central PMCID: PMC5870671.
- [Docker](https://dl.acm.org/doi/10.5555/2600239.2600241)
- [Singularity](https://pubmed.ncbi.nlm.nih.gov/28494014/)
> Kurtzer GM, Sochat V, Bauer MW. Singularity: Scientific containers for mobility of compute. PLoS One. 2017 May 11;12(5):e0177459. doi: 10.1371/journal.pone.0177459. eCollection 2017. PubMed PMID: 28494014; PubMed Central PMCID: PMC5426675.