From Wikipedia, the free encyclopedia

Regarding "Undisclosed payments" allegation

Thanks for being so observant to notice that I have made a major overhaul of this article draft. I see, why this edit might raise some concerns regarding undisclosed payments, but rest assured that I have not received any payments or other benefits in exchange for this edit. Therefore, I deny those accusations.

Please allow me to elaborate on my background and the motivation for working on this article: While I do not have a user page on the English Wikipedia, I do have one on the German Wikipedia as well as on Wikimedia Commons. I have been contributing to both since 2007, when I was an undergrad student at the university. I have mostly ceased from contributing to Wikipedia due to time constraints by now, but of course continue to cherish the project.

When I learned that an academic collaborator of mine wanted to add an article for Nextflow to Wikipedia, I was thrilled. It had never occurred to me, but I was immediately convinced that this is a good idea, because it is a very important tool for our research work and students might want to look it up when it is mentioned e.g. in the method section of scientific publications. However, I had to agree with Onel5969, that the article in its previous form was written too promotional and partly incomprehensible. So I sacrificed a free afternoon (and unintentionally also the evening) to fix the (in my opinion) most blatant issues. Admittedly, it was way more work than what I initially wanted to put into the edit, but I also couldn't stop halfway through either, since I eventually ended up changing the entire structure.

I have tried to incorporate the criticisms expressed to the best of my ability, but agree that there should be an external review to ensure that haven't been too sympathetic with the subject. However, the suspicion that

Conflict of interest statement: I am employed by the Swedish National Genomics Infrastructure, which co-founded the nf-core community. Phil Ewels is a former colleague of mine, and I have met other core Nextflow/nf-core contributors at scientific conferences. I work with Nextflow daily, and it is fundamental for my work. However, I have not received any payments or other benefits for editing the article, and it was my own decision to devote my spare time to edit. I have no investments in or affiliations with Sequera, the spin-off company that maintains Nextflow. My real name is Matthias Zepper, which you can use to verify this information.

-- Curnen ( talk) 17:23, 6 December 2022 (UTC) reply

Additional references

Since the lack of references to substantiate the importance of Nextflow as notable scientific workflow system has been criticized twice, I have spent a whole Saturday gathering the scientific publications of numerous pipelines written in Nextflow. I appreciate that this is too much clutter for the main article, but before anyone criticizes for the third time that sources don't exist, I'd like to keep them around here for future reference.

The claim that Over the last five years, numerous pipelines for many different applications and analyses in the field of genomics have been published is backed by those references:

[1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] [21] [22] [23] [24] [25] [26] [27] [28] [29] [30] [31] [32] [33] [34] [35] [36] [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] [47] [48] [49] Curnen ( talk) 10:35, 2 February 2023 (UTC) reply

References

  1. ^ Song, Zeyuan; Gurinovich, Anastasia; Federico, Anthony; Monti, Stefano; Sebastiani, Paola (2021). "Nf-gwas-pipeline: A Nextflow Genome-Wide Association Study Pipeline". Journal of Open Source Software. 6 (59): 2957. Bibcode: 2021JOSS....6.2957S. doi: 10.21105/joss.02957. PMC  9137404. PMID  35647481.
  2. ^ Twesigomwe, David; Drögemöller, Britt I.; Wright, Galen E.B.; Siddiqui, Azra; Rocha, Jorge; Lombard, Zané; Hazelhurst, Scott (2021). "StellarPGx: A Nextflow Pipeline for Calling Star Alleles in Cytochrome P450 Genes". Clinical Pharmacology & Therapeutics. 110 (3): 741–749. doi: 10.1002/cpt.2173. PMID  33492672. S2CID  231704161.
  3. ^ Hölzer, Martin; Marz, Manja (2021). "PoSei Don: A Nextflow pipeline for the detection of evolutionary recombination events and positive selection". Bioinformatics. 37 (7): 1018–1020. doi: 10.1093/bioinformatics/btaa695. PMID  32735310.
  4. ^ Hu, Kai; Liu, Haibo; Lawson, Nathan D.; Zhu, Lihua Julie (2022). "ScATACpipe: A nextflow pipeline for comprehensive and reproducible analyses of single cell ATAC-seq data". Frontiers in Cell and Developmental Biology. 10: 981859. doi: 10.3389/fcell.2022.981859. PMC  9551270. PMID  36238687.
  5. ^ Mpangase, Phelelani; Frost, Jacqueline; Tikly, Mohammed; Ramsay, Michèle; Hazelhurst, Scott (2021). "Nf-rnaSeq Count: A Nextflow pipeline for obtaining raw read counts from RNA-seq data". South African Computer Journal. 33 (2). doi: 10.18489/sacj.v33i2.830. PMC  9097006. PMID  35574063.
  6. ^ Bao, Xiaoqiong; Zhu, Kaiyu; Liu, Xuefei; Chen, Zhihang; Luo, Ziwei; Zhao, Qi; Ren, Jian; Zuo, Zhixiang (2022). "MeRIPseq Pipe: An integrated analysis pipeline for MeRIP-seq data based on Nextflow". Bioinformatics. 38 (7): 2054–2056. doi: 10.1093/bioinformatics/btac025. PMID  35022687.
  7. ^ Van De Sande, Bram; Flerin, Christopher; Davie, Kristofer; De Waegeneer, Maxime; Hulselmans, Gert; Aibar, Sara; Seurinck, Ruth; Saelens, Wouter; Cannoodt, Robrecht; Rouchon, Quentin; Verbeiren, Toni; De Maeyer, Dries; Reumers, Joke; Saeys, Yvan; Aerts, Stein (2020). "A scalable SCENIC workflow for single-cell gene regulatory network analysis". Nature Protocols. 15 (7): 2247–2276. doi: 10.1038/s41596-020-0336-2. PMID  32561888. S2CID  219935802.
  8. ^ Liu, Xiaochuan; Bienkowska, Jadwiga R.; Zhong, Wenyan (2020). "GeneTEFlow: A Nextflow-based pipeline for analysing gene and transposable elements expression from RNA-Seq data". PLOS ONE. 15 (8): e0232994. Bibcode: 2020PLoSO..1532994L. doi: 10.1371/journal.pone.0232994. PMC  7458328. PMID  32866155.
  9. ^ Lataretu, Marie; Hölzer, Martin (2020). "RNAflow: An Effective and Simple RNA-Seq Differential Gene Expression Pipeline Using Nextflow". Genes. 11 (12): 1487. doi: 10.3390/genes11121487. PMC  7763471. PMID  33322033.
  10. ^ Zhao, Qi; Sun, Yu; Wang, Dawei; Zhang, Hongwan; Yu, Kai; Zheng, Jian; Zuo, Zhixiang (2018). "LNC Pipe: A Nextflow-based pipeline for identification and analysis of long non-coding RNAs from RNA-Seq data". Journal of Genetics and Genomics. 45 (7): 399–401. doi: 10.1016/j.jgg.2018.06.005. PMID  30055874. S2CID  51865348.
  11. ^ Gordon, M. Grace; Inoue, Fumitaka; Martin, Beth; Schubach, Max; Agarwal, Vikram; Whalen, Sean; Feng, Shiyun; Zhao, Jingjing; Ashuach, Tal; Ziffra, Ryan; Kreimer, Anat; Georgakopoulos-Soares, Ilias; Yosef, Nir; Ye, Chun Jimmie; Pollard, Katherine S.; Shendure, Jay; Kircher, Martin; Ahituv, Nadav (2020). "LentiMPRA and MPRAflow for high-throughput functional characterization of gene regulatory elements". Nature Protocols. 15 (8): 2387–2412. doi: 10.1038/s41596-020-0333-5. PMC  7550205. PMID  32641802.
  12. ^ Mousavi‐Derazmahalleh, Mahsa; Stott, Audrey; Lines, Rose; Peverley, Georgia; Nester, Georgia; Simpson, Tiffany; Zawierta, Michal; de la Pierre, Marco; Bunce, Michael; Christophersen, Claus T. (2021). "EDNAFlow, an automated, reproducible and scalable workflow for analysis of environmental DNA sequences exploiting Nextflow and Singularity" (PDF). Molecular Ecology Resources. 21 (5): 1697–1704. doi: 10.1111/1755-0998.13356. PMID  33580619. S2CID  231910408.
  13. ^ Armstrong, Ellie E.; Campana, Michael G. (2023). "Rates Tools: A Nextflow pipeline for detecting de novo germline mutations in pedigree sequence data". Bioinformatics. 39 (1). doi: 10.1093/bioinformatics/btac784. PMID  36469327.
  14. ^ Steinig, Eike; Duchêne, Sebastián; Aglua, Izzard; Greenhill, Andrew; Ford, Rebecca; Yoannes, Mition; Jaworski, Jan; Drekore, Jimmy; Urakoko, Bohu; Poka, Harry; Wurr, Clive; Ebos, Eri; Nangen, David; Manning, Laurens; Laman, Moses; Firth, Cadhla; Smith, Simon; Pomat, William; Tong, Steven Y C.; Coin, Lachlan; McBryde, Emma; Horwood, Paul (2022). "Phylodynamic Inference of Bacterial Outbreak Parameters Using Nanopore Sequencing". Molecular Biology and Evolution. 39 (3). doi: 10.1093/molbev/msac040. PMC  8963328. PMID  35171290.
  15. ^ Rodríguez-Pérez, Héctor; Ciuffreda, Laura; Flores, Carlos (2022). "NanoRTax, a real-time pipeline for taxonomic and diversity analysis of nanopore 16S rRNA amplicon sequencing data". Computational and Structural Biotechnology Journal. 20: 5350–5354. doi: 10.1016/j.csbj.2022.09.024. PMC  9522874. PMID  36212537.
  16. ^ Brandenburg, Jean-Tristan; Clark, Lindsay; Botha, Gerrit; Panji, Sumir; Baichoo, Shakuntala; Fields, Christopher; Hazelhurst, Scott (2022). "H3AGWAS: A portable workflow for genome wide association studies". BMC Bioinformatics. 23 (1): 498. doi: 10.1186/s12859-022-05034-w. PMC  9675212. PMID  36402955.{{ cite journal}}: CS1 maint: unflagged free DOI ( link)
  17. ^ Bremges, Andreas; Fritz, Adrian; McHardy, Alice C. (2020). "CAMITAX: Taxon labels for microbial genomes". GigaScience. 9 (1). doi: 10.1093/gigascience/giz154. PMC  6946028. PMID  31909794.
  18. ^ Talenti, Andrea; Prendergast, James (2021). "Nf-LO: A Scalable, Containerized Workflow for Genome-to-Genome Lift over". Genome Biology and Evolution. 13 (9). doi: 10.1093/gbe/evab183. PMC  8412297. PMID  34383887.
  19. ^ Cornet, Luc; Ahn, Anne-Catherine; Wilmotte, Annick; Baurain, Denis (2021). "ORPER: A Workflow for Constrained SSU rRNA Phylogenies". Genes. 12 (11): 1741. doi: 10.3390/genes12111741. PMC  8623055. PMID  34828348.
  20. ^ Marquet, Mike; Hölzer, Martin; Pletz, Mathias W.; Viehweger, Adrian; Makarewicz, Oliwia; Ehricht, Ralf; Brandt, Christian (2022). "What the Phage: A scalable workflow for the identification and analysis of phage sequences". GigaScience. 11. doi: 10.1093/gigascience/giac110. PMC  9673492. PMID  36399058.
  21. ^ Schmal, Matthias; Girod, Crystal; Yaver, Debbie; Mach, Robert L; Mach-Aigner, Astrid R (2022). "A bioinformatic-assisted workflow for genome-wide identification of ncRNAs". Nar Genomics and Bioinformatics. 4 (3): lqac059. doi: 10.1093/nargab/lqac059. PMC  9376865. PMID  35979446.
  22. ^ Albanese, Davide; Donati, Claudio (2021). "Large-scale quality assessment of prokaryotic genomes with metashot/Prok-quality". F1000Research. 10: 822. doi: 10.12688/f1000research.54418.1. PMC  8804904. PMID  35136576.{{ cite journal}}: CS1 maint: unflagged free DOI ( link)
  23. ^ Carpanzano, Simone; Santorsola, Mariangela; Lescai, Francesco; Lescai, F. (2022). "Hgtseq: A Standard Pipeline to Study Horizontal Gene Transfer". International Journal of Molecular Sciences. 23 (23): 14512. doi: 10.3390/ijms232314512. PMC  9738810. PMID  36498841.
  24. ^ Hadish, John A.; Biggs, Tyler D.; Shealy, Benjamin T.; Bender, M. Reed; McKnight, Coleman B.; Wytko, Connor; Smith, Melissa C.; Feltus, F. Alex; Honaas, Loren; Ficklin, Stephen P. (2022). "GEMmaker: Process massive RNA-seq datasets on heterogeneous computational infrastructure". BMC Bioinformatics. 23 (1): 156. doi: 10.1186/s12859-022-04629-7. PMC  9063052. PMID  35501696.{{ cite journal}}: CS1 maint: unflagged free DOI ( link)
  25. ^ Cope, Alexander L.; Anderson, Felicity; Favate, John; Jackson, Michael; Mok, Amanda; Kurowska, Anna; Liu, Junchen; MacKenzie, Emma; Shivakumar, Vikram; Tilton, Peter; Winterbourne, Sophie M.; Xue, Siyin; Kavoussanakis, Kostas; Lareau, Liana F.; Shah, Premal; Wallace, Edward W J. (2022). "Riboviz 2: A flexible and robust ribosome profiling data analysis and visualization workflow". Bioinformatics. 38 (8): 2358–2360. doi: 10.1093/bioinformatics/btac093. PMC  9004635. PMID  35157051.
  26. ^ Rivera‐Vicéns, Ramón E.; Garcia‐Escudero, Catalina A.; Conci, Nicola; Eitel, Michael; Wörheide, Gert (2022). "Trans Pi—a comprehensive TRanscriptome ANalysiS PIpeline for de novo transcriptome assembly". Molecular Ecology Resources. 22 (5): 2070–2086. doi: 10.1111/1755-0998.13593. PMID  35119207. S2CID  231980763.
  27. ^ Márquez, Yamile; Mantica, Federica; Cozzuto, Luca; Burguera, Demian; Hermoso-Pulido, Antonio; Ponomarenko, Julia; Roy, Scott W.; Irimia, Manuel (2021). "Ex Orthist: A tool to infer exon orthologies at any evolutionary distance". Genome Biology. 22 (1): 239. doi: 10.1186/s13059-021-02441-9. PMC  8379844. PMID  34416914.{{ cite journal}}: CS1 maint: unflagged free DOI ( link)
  28. ^ Sensalari, Cecilia; Maere, Steven; Lohaus, Rolf (2022). "Ksrates: Positioning whole-genome duplications relative to speciation events in KS distributions". Bioinformatics. 38 (2): 530–532. doi: 10.1093/bioinformatics/btab602. PMID  34406368.
  29. ^ Vromman, Marieke; Anckaert, Jasper; Vandesompele, Jo; Volders, Pieter-Jan (2022). "CIRCprimerXL: Convenient and High-Throughput PCR Primer Design for Circular RNA Quantification". Frontiers in Bioinformatics. 2: 834655. doi: 10.3389/fbinf.2022.834655. PMC  9580850. PMID  36304334.
  30. ^ Brandt, Christian; Krautwurst, Sebastian; Spott, Riccardo; Lohde, Mara; Jundzill, Mateusz; Marquet, Mike; Hölzer, Martin (2022). "Corrigendum: Pore Cov - an Easy to Use, Fast, and Robust Workflow for SARS CoV-2 Genome Reconstruction via Nanopore Sequencing". Frontiers in Genetics. 13: 875644. doi: 10.3389/fgene.2022.875644. PMC  8964395. PMID  35368706.
  31. ^ Van Damme, Renaud; Hölzer, Martin; Viehweger, Adrian; Müller, Bettina; Bongcam-Rudloff, Erik; Brandt, Christian (2021). "Metagenomics workflow for hybrid assembly, differential coverage binning, metatranscriptomics and pathway analysis (MUFFIN)". PLOS Computational Biology. 17 (2): e1008716. Bibcode: 2021PLSCB..17E8716V. doi: 10.1371/journal.pcbi.1008716. PMC  7899367. PMID  33561126.{{ cite journal}}: CS1 maint: unflagged free DOI ( link)
  32. ^ Titmuss, Emma; Corbett, Richard D.; Davidson, Scott; Abbasi, Sanna; Williamson, Laura M.; Pleasance, Erin D.; Shlien, Adam; Renouf, Daniel J.; Jones, Steven J. M.; Laskin, Janessa; Marra, Marco A. (2022). "TMBur: A distributable tumor mutation burden approach for whole genome sequencing". BMC Medical Genomics. 15 (1): 190. doi: 10.1186/s12920-022-01348-z. PMC  9450342. PMID  36071521.{{ cite journal}}: CS1 maint: unflagged free DOI ( link)
  33. ^ Vasilopoulou, Christina; Wingfield, Benjamin; Morris, Andrew P.; Duddy, William (2021). "SNPQT: Flexible, reproducible, and comprehensive quality control and imputation of genomic data". F1000Research. 10: 567. doi: 10.12688/f1000research.53821.2. PMC  8637247. PMID  34900230.{{ cite journal}}: CS1 maint: unflagged free DOI ( link)
  34. ^ Senkin, Sergey (2021). "MSA: Reproducible mutational signature attribution with confidence based on simulations". BMC Bioinformatics. 22 (1): 540. doi: 10.1186/s12859-021-04450-8. PMC  8567580. PMID  34736398.{{ cite journal}}: CS1 maint: unflagged free DOI ( link)
  35. ^ Shafranskaya, Daria; Kale, Varsha; Finn, Rob; Lapidus, Alla L.; Korobeynikov, Anton; Prjibelski, Andrey D. (2022). "MetaGT: A pipeline for de novo assembly of metatranscriptomes with the aid of metagenomic data". Frontiers in Microbiology. 13: 981458. doi: 10.3389/fmicb.2022.981458. PMC  9651917. PMID  36386613.
  36. ^ Bryzghalov, Oleksii; Makałowska, Izabela; Szcześniak, Michał Wojciech (2021). "LNC Evo: Automated identification and conservation study of long noncoding RNAs". BMC Bioinformatics. 22 (1): 59. doi: 10.1186/s12859-021-03991-2. PMC  7871587. PMID  33563213.{{ cite journal}}: CS1 maint: unflagged free DOI ( link)
  37. ^ Farkas, Carlos; Recabal, Antonia; Mella, Andy; Candia-Herrera, Daniel; Olivero, Maryori González; Haigh, Jody Jonathan; Tarifeño-Saldivia, Estefanía; Caprile, Teresa (2022). "Annotate_my_genomes: An easy-to-use pipeline to improve genome annotation and uncover neglected genes by hybrid RNA sequencing". GigaScience. 11. doi: 10.1093/gigascience/giac099. PMC  9724561. PMID  36472574.
  38. ^ Kässens, Jan Christian; Wienbrandt, Lars; Ellinghaus, David (2021). "BIGwas: Single-command quality control and association testing for multi-cohort and biobank-scale GWAS/PheWAS data". GigaScience. 10 (6). doi: 10.1093/gigascience/giab047. PMC  8239664. PMID  34184051.
  39. ^ Donovan, Paul D.; McHale, Natalie M.; Venø, Morten T.; Prehn, Jochen H M. (2021). "TsRNAsearch: A pipeline for the identification of tRNA and ncRNA fragments from small RNA-sequencing data". Bioinformatics. 37 (23): 4424–4430. doi: 10.1093/bioinformatics/btab515. PMID  34255836.
  40. ^ Lexa, Matej; Cechova, Monika; Nguyen, Son Hoang; Jedlicka, Pavel; Tokan, Viktor; Kubat, Zdenek; Hobza, Roman; Kejnovsky, Eduard (2022). "HiC-TE: A computational pipeline for Hi-C data analysis to study the role of repeat family interactions in the genome 3D organization". Bioinformatics. 38 (16): 4030–4032. doi: 10.1093/bioinformatics/btac442. PMID  35781332.
  41. ^ Murigneux, Valentine; Roberts, Leah W.; Forde, Brian M.; Phan, Minh-Duy; Nhu, Nguyen Thi Khanh; Irwin, Adam D.; Harris, Patrick N. A.; Paterson, David L.; Schembri, Mark A.; Whiley, David M.; Beatson, Scott A. (2021). "MicroPIPE: Validating an end-to-end workflow for high-quality complete bacterial genome construction". BMC Genomics. 22 (1): 474. doi: 10.1186/s12864-021-07767-z. PMC  8235852. PMID  34172000.{{ cite journal}}: CS1 maint: unflagged free DOI ( link)
  42. ^ Grassi, Luigi; Harris, Claire; Zhu, Jie; Hardman, Colin; Hatton, Diane (2021). "DetectIS: A pipeline to rapidly detect exogenous DNA integration sites using DNA or RNA paired-end sequencing data". Bioinformatics. 37 (22): 4230–4232. doi: 10.1093/bioinformatics/btab366. PMC  9502153. PMID  33978747.
  43. ^ Crook, Derrick; Volk, Denis; Yang-Turner, Fan; Xu, Yifei (2020). "NanoSPC: A scalable, portable, cloud compatible viral nanopore metagenomic data processing pipeline". Nucleic Acids Research. 48 (W1): W366–W371. doi: 10.1093/nar/gkaa413. PMC  7319573. PMID  32442274.
  44. ^ Miller, Brecca R.; Morse, Alison M.; Borgert, Jacqueline E.; Liu, Zihao; Sinclair, Kelsey; Gamble, Gavin; Zou, Fei; Newman, Jeremy R B.; León-Novelo, Luis G.; Marroni, Fabio; McIntyre, Lauren M. (2021). "Testcrosses are an efficient strategy for identifying cis-regulatory variation: Bayesian analysis of allele-specific expression (BayesASE)". G3 Genes|Genomes|Genetics. 11 (5). doi: 10.1093/g3journal/jkab096. PMC  8104932. PMID  33772539.
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  49. ^ Roe, David; Kuang, Rui (2020). "Accurate and Efficient KIR Gene and Haplotype Inference from Genome Sequencing Reads with Novel K-mer Signatures". Frontiers in Immunology. 11: 583013. doi: 10.3389/fimmu.2020.583013. PMC  7727328. PMID  33324401.
From Wikipedia, the free encyclopedia

Regarding "Undisclosed payments" allegation

Thanks for being so observant to notice that I have made a major overhaul of this article draft. I see, why this edit might raise some concerns regarding undisclosed payments, but rest assured that I have not received any payments or other benefits in exchange for this edit. Therefore, I deny those accusations.

Please allow me to elaborate on my background and the motivation for working on this article: While I do not have a user page on the English Wikipedia, I do have one on the German Wikipedia as well as on Wikimedia Commons. I have been contributing to both since 2007, when I was an undergrad student at the university. I have mostly ceased from contributing to Wikipedia due to time constraints by now, but of course continue to cherish the project.

When I learned that an academic collaborator of mine wanted to add an article for Nextflow to Wikipedia, I was thrilled. It had never occurred to me, but I was immediately convinced that this is a good idea, because it is a very important tool for our research work and students might want to look it up when it is mentioned e.g. in the method section of scientific publications. However, I had to agree with Onel5969, that the article in its previous form was written too promotional and partly incomprehensible. So I sacrificed a free afternoon (and unintentionally also the evening) to fix the (in my opinion) most blatant issues. Admittedly, it was way more work than what I initially wanted to put into the edit, but I also couldn't stop halfway through either, since I eventually ended up changing the entire structure.

I have tried to incorporate the criticisms expressed to the best of my ability, but agree that there should be an external review to ensure that haven't been too sympathetic with the subject. However, the suspicion that

Conflict of interest statement: I am employed by the Swedish National Genomics Infrastructure, which co-founded the nf-core community. Phil Ewels is a former colleague of mine, and I have met other core Nextflow/nf-core contributors at scientific conferences. I work with Nextflow daily, and it is fundamental for my work. However, I have not received any payments or other benefits for editing the article, and it was my own decision to devote my spare time to edit. I have no investments in or affiliations with Sequera, the spin-off company that maintains Nextflow. My real name is Matthias Zepper, which you can use to verify this information.

-- Curnen ( talk) 17:23, 6 December 2022 (UTC) reply

Additional references

Since the lack of references to substantiate the importance of Nextflow as notable scientific workflow system has been criticized twice, I have spent a whole Saturday gathering the scientific publications of numerous pipelines written in Nextflow. I appreciate that this is too much clutter for the main article, but before anyone criticizes for the third time that sources don't exist, I'd like to keep them around here for future reference.

The claim that Over the last five years, numerous pipelines for many different applications and analyses in the field of genomics have been published is backed by those references:

[1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] [21] [22] [23] [24] [25] [26] [27] [28] [29] [30] [31] [32] [33] [34] [35] [36] [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] [47] [48] [49] Curnen ( talk) 10:35, 2 February 2023 (UTC) reply

References

  1. ^ Song, Zeyuan; Gurinovich, Anastasia; Federico, Anthony; Monti, Stefano; Sebastiani, Paola (2021). "Nf-gwas-pipeline: A Nextflow Genome-Wide Association Study Pipeline". Journal of Open Source Software. 6 (59): 2957. Bibcode: 2021JOSS....6.2957S. doi: 10.21105/joss.02957. PMC  9137404. PMID  35647481.
  2. ^ Twesigomwe, David; Drögemöller, Britt I.; Wright, Galen E.B.; Siddiqui, Azra; Rocha, Jorge; Lombard, Zané; Hazelhurst, Scott (2021). "StellarPGx: A Nextflow Pipeline for Calling Star Alleles in Cytochrome P450 Genes". Clinical Pharmacology & Therapeutics. 110 (3): 741–749. doi: 10.1002/cpt.2173. PMID  33492672. S2CID  231704161.
  3. ^ Hölzer, Martin; Marz, Manja (2021). "PoSei Don: A Nextflow pipeline for the detection of evolutionary recombination events and positive selection". Bioinformatics. 37 (7): 1018–1020. doi: 10.1093/bioinformatics/btaa695. PMID  32735310.
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