# nf-core/funcscan: Citations

## [nf-core](https://pubmed.ncbi.nlm.nih.gov/32055031/)

> Ewels, P. A., Peltzer, A., Fillinger, S., Patel, H., Alneberg, J., Wilm, A., Garcia, M. U., Di Tommaso, P., & Nahnsen, S. (2020). The nf-core framework for community-curated bioinformatics pipelines. Nature biotechnology, 38(3), 276–278. [DOI: 10.1038/s41587-020-0439-x](https://doi.org/10.1038/s41587-020-0439-x)

## [Nextflow](https://pubmed.ncbi.nlm.nih.gov/28398311/)

> Di Tommaso, P., Chatzou, M., Floden, E. W., Barja, P. P., Palumbo, E., & Notredame, C. (2017). Nextflow enables reproducible computational workflows. Nature biotechnology, 35(4), 316–319. [DOI: 10.1038/nbt.3820](https://doi.org/10.1038/nbt.3820)

## Pipeline tools

- [ABRicate](https://github.com/tseemann/abricate)

  > Seemann, T. (2020). ABRicate. Github [https://github.com/tseemann/abricate](https://github.com/tseemann/abricate).

- [AMPir](https://doi.org/10.1093/bioinformatics/btaa653)

  > Fingerhut, L., Miller, D. J., Strugnell, J. M., Daly, N. L., & Cooke, I. R. (2021). ampir: an R package for fast genome-wide prediction of antimicrobial peptides. Bioinformatics (Oxford, England), 36(21), 5262–5263. [DOI: 10.1093/bioinformatics/btaa653](https://doi.org/10.1093/bioinformatics/btaa653)

- [AMPlify](https://doi.org/10.1186/s12864-022-08310-4)

  > CLi, C., Sutherland, D., Hammond, S. A., Yang, C., Taho, F., Bergman, L., Houston, S., Warren, R. L., Wong, T., Hoang, L., Cameron, C. E., Helbing, C. C., & Birol, I. (2022). AMPlify: attentive deep learning model for discovery of novel antimicrobial peptides effective against WHO priority pathogens. BMC genomics, 23(1), 77. [DOI: 10.1186/s12864-022-08310-4](https://doi.org/10.1186/s12864-022-08310-4)

- [AMRFinderPlus](https://doi.org/10.1038/s41598-021-91456-0)

  > Feldgarden, M., Brover, V., Gonzalez-Escalona, N., Frye, J. G., Haendiges, J., Haft, D. H., Hoffmann, M., Pettengill, J. B., Prasad, A. B., Tillman, G. E., Tyson, G. H., & Klimke, W. (2021). AMRFinderPlus and the Reference Gene Catalog facilitate examination of the genomic links among antimicrobial resistance, stress response, and virulence. Scientific reports, 11(1), 12728. [DOI: 10.1038/s41598-021-91456-0](https://doi.org/10.1038/s41598-021-91456-0)

- [AntiSMASH](https://doi.org/10.1093/nar/gkab335)

  > Blin, K., Shaw, S., Kloosterman, A. M., Charlop-Powers, Z., van Wezel, G. P., Medema, M. H., & Weber, T. (2021). antiSMASH 6.0: improving cluster detection and comparison capabilities. Nucleic acids research, 49(W1), W29–W35. [DOI: 10.1093/nar/gkab335](https://doi.org/10.1093/nar/gkab335)

- [Bakta](https://doi.org/10.1099/mgen.0.000685)

  > 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). [DOI: 10.1099/mgen.0.000685](https://doi.org/10.1099/mgen.0.000685)

- [DeepARG](https://doi.org/10.1186/s40168-018-0401-z)

  > Arango-Argoty, G., Garner, E., Pruden, A., Heath, L. S., Vikesland, P., & Zhang, L. (2018). DeepARG: a deep learning approach for predicting antibiotic resistance genes from metagenomic data. Microbiome, 6(1), 23. [DOI: 10.1186/s40168-018-0401-z](https://doi.org/10.1186/s40168-018-0401-z)

- [DeepBGC](https://doi.org/10.1093/nar/gkz654)

  > Hannigan, G. D., Prihoda, D., Palicka, A., Soukup, J., Klempir, O., Rampula, L., Durcak, J., Wurst, M., Kotowski, J., Chang, D., Wang, R., Piizzi, G., Temesi, G., Hazuda, D. J., Woelk, C. H., & Bitton, D. A. (2019). A deep learning genome-mining strategy for biosynthetic gene cluster prediction. Nucleic acids research, 47(18), e110. [DOI: 10.1093/nar/gkz654](https://doi.org/10.1093/nar/gkz654)

- [fARGene](https://doi.org/10.1186/s40168-019-0670-1)

  > Berglund, F., Österlund, T., Boulund, F., Marathe, N. P., Larsson, D., & Kristiansson, E. (2019). Identification and reconstruction of novel antibiotic resistance genes from metagenomes. Microbiome, 7(1), 52. [DOI: 10.1186/s40168-019-0670-1](https://doi.org/10.1186/s40168-019-0670-1)

- [GECCO](https://gecco.embl.de)

  > Carroll, L. M. , Larralde, M., Fleck, J. S., Ponnudurai, R., Milanese, A., Cappio Barazzone, E. & Zeller, G. (2021). Accurate de novo identification of biosynthetic gene clusters with GECCO. bioRxiv [DOI: 10.1101/2021.05.03.442509](https://doi.org/10.1101/2021.05.03.442509)

- [hAMRonization](https://github.com/pha4ge/hAMRonization)

  > Public Health Alliance for Genomic Epidemiology (pha4ge). (2022). Parse multiple Antimicrobial Resistance Analysis Reports into a common data structure. Github. Retrieved October 5, 2022, from [https://github.com/pha4ge/hAMRonization](https://github.com/pha4ge/hAMRonization)

- [AMPcombi](https://github.com/Darcy220606/AMPcombi)

  > Ibrahim, A. & Perelo, L. (2023). Darcy220606/AMPcombi. [DOI: 10.5281/zenodo.7639121](https://doi.org/10.5281/zenodo.7639121).

- [HMMER](https://doi.org/10.1371/journal.pcbi.1002195.)

  > Eddy S. R. (2011). Accelerated Profile HMM Searches. PLoS computational biology, 7(10), e1002195. [DOI: 10.1371/journal.pcbi.1002195](https://doi.org/10.1371/journal.pcbi.1002195)

- [Macrel](https://doi.org/10.7717/peerj.10555)

  > Santos-Júnior, C. D., Pan, S., Zhao, X. M., & Coelho, L. P. (2020). Macrel: antimicrobial peptide screening in genomes and metagenomes. PeerJ, 8, e10555. [DOI: 10.7717/peerj.10555](https://doi.org/10.7717/peerj.10555)

- [Prodigal](https://doi.org/10.1186/1471-2105-11-119)

  > Hyatt, D., Chen, G. L., Locascio, P. F., Land, M. L., Larimer, F. W., & Hauser, L. J. (2010). Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC bioinformatics, 11, 119. [DOI: 10.1186/1471-2105-11-119](https://doi.org/10.1186/1471-2105-11-119)

- [PROKKA](https://doi.org/10.1093/bioinformatics/btu153)

  > Seemann, T. (2014). Prokka: rapid prokaryotic genome annotation. Bioinformatics (Oxford, England), 30(14), 2068–2069. [DOI: 10.1093/bioinformatics/btu153](https://doi.org/10.1093/bioinformatics/btu153)

- [Pyrodigal](https://doi.org/10.1186/1471-2105-11-119)

  > Larralde, M. (2022). Pyrodigal: Python bindings and interface to Prodigal, an efficient method for gene prediction in prokaryotes. Journal of Open Source Software, 7(72), 4296. [DOI: 10.21105/joss.04296](https://doi.org/10.21105/joss.04296)

- [RGI](https://doi.org/10.1093/nar/gkz935)

  > Alcock, B. P., Raphenya, A. R., Lau, T., Tsang, K. K., Bouchard, M., Edalatmand, A., Huynh, W., Nguyen, A. V., Cheng, A. A., Liu, S., Min, S. Y., Miroshnichenko, A., Tran, H. K., Werfalli, R. E., Nasir, J. A., Oloni, M., Speicher, D. J., Florescu, A., Singh, B., Faltyn, M., … McArthur, A. G. (2020). CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database. Nucleic acids research, 48(D1), D517–D525. [DOI: 10.1093/nar/gkz935](https://doi.org/10.1093/nar/gkz935)

## Software packaging/containerisation tools

- [Anaconda](https://anaconda.com)

  > Anaconda Software Distribution. Computer software. Vers. 2-2.4.0. Anaconda, Nov. 2016. Web.

- [Bioconda](https://pubmed.ncbi.nlm.nih.gov/29967506/)

  > Grüning, B., Dale, R., Sjödin, A., Chapman, B. A., Rowe, J., Tomkins-Tinch, C. H., Valieris, R., Köster, J., & Bioconda Team (2018). Bioconda: sustainable and comprehensive software distribution for the life sciences. Nature methods, 15(7), 475–476. [DOI: 10.1038/s41592-018-0046-7](https://doi.org/10.1038/s41592-018-0046-7)

- [BioContainers](https://pubmed.ncbi.nlm.nih.gov/28379341/)

  > da Veiga Leprevost, F., Grüning, B. A., Alves Aflitos, S., Röst, H. L., Uszkoreit, J., Barsnes, H., Vaudel, M., Moreno, P., Gatto, L., Weber, J., Bai, M., Jimenez, R. C., Sachsenberg, T., Pfeuffer, J., Vera Alvarez, R., Griss, J., Nesvizhskii, A. I., & Perez-Riverol, Y. (2017). BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics (Oxford, England), 33(16), 2580–2582. [DOI: 10.1093/bioinformatics/btx192](https://doi.org/10.1093/bioinformatics/btx192)

- [Docker](https://dl.acm.org/doi/10.5555/2600239.2600241)

- [Singularity](https://pubmed.ncbi.nlm.nih.gov/28494014/)
  > Kurtzer, G. M., Sochat, V., & Bauer, M. W. (2017). Singularity: Scientific containers for mobility of compute. PloS one, 12(5), e0177459. [DOI: 10.1371/journal.pone.0177459](https://doi.org/10.1371/journal.pone.0177459)
