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ebi-metagenomics/mettannotator: Citations

mettannotator: a comprehensive and scalable Nextflow annotation pipeline for prokaryotic assemblies (pre-print)

Gurbich TA, Beracochea M, De Silva NH, Finn RD. mettannotator: a comprehensive and scalable Nextflow annotation pipeline for prokaryotic assemblies. doi: https://doi.org/10.1101/2024.07.11.603040

MGnify Genomes

Gurbich TA, Almeida A, Beracochea M, Burdett T, Burgin J, Cochrane G, Raj S, Richardson L, Rogers AB, Sakharova E, Salazar GA and Finn RD. MGnify Genomes: A Resource for Biome-specific Microbial Genome Catalogues. J Mol Biol. 2023 Jul; 435(14). doi: https://doi.org/10.1016/j.jmb.2023.168016. PubMed PMID:

nf-core

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

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

  • MultiQC

    Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924.

  • Prokka

    Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics. 2014 Jul 15;30(14):2068-9. doi: 10.1093/bioinformatics/btu153. Epub 2014 Mar 18. PMID: 24642063.

  • Bakta

    Schwengers O, Jelonek L, Dieckmann MA, Beyvers S, Blom J, Goesmann A. Bakta: rapid and standardized annotation of bacterial genomes via alignment-free sequence identification. Microb Genom. 2021 Nov;7(11):000685. doi: 10.1099/mgen.0.000685. PMID: 34739369; PMCID: PMC8743544.

  • InterProScan

    Jones P, Binns D, Chang HY, Fraser M, Li W, McAnulla C, McWilliam H, Maslen J, Mitchell A, Nuka G, Pesseat S, Quinn AF, Sangrador-Vegas A, Scheremetjew M, Yong SY, Lopez R, Hunter S. InterProScan 5: genome-scale protein function classification. Bioinformatics. 2014 May 1;30(9):1236-40. doi: 10.1093/bioinformatics/btu031. Epub 2014 Jan 21. PMID: 24451626; PMCID: PMC3998142.

  • eggNOG-mapper

    Cantalapiedra CP, Hernández-Plaza A, Letunic I, Bork P, Huerta-Cepas J. eggNOG-mapper v2: Functional Annotation, Orthology Assignments, and Domain Prediction at the Metagenomic Scale. Mol Biol Evol. 2021 Dec 9;38(12):5825-5829. doi: 10.1093/molbev/msab293. PMID: 34597405; PMCID: PMC8662613.

  • UniFIRE

    MacDougall A, Volynkin V, Saidi R, Poggioli D, Zellner H, Hatton-Ellis E, Joshi V, O'Donovan C, Orchard S, Auchincloss AH, Baratin D, Bolleman J, Coudert E, de Castro E, Hulo C, Masson P, Pedruzzi I, Rivoire C, Arighi C, Wang Q, Chen C, Huang H, Garavelli J, Vinayaka CR, Yeh LS, Natale DA, Laiho K, Martin MJ, Renaux A, Pichler K; UniProt Consortium. UniRule: a unified rule resource for automatic annotation in the UniProt Knowledgebase. Bioinformatics. 2020 Nov 1;36(17):4643-4648. doi: 10.1093/bioinformatics/btaa485. Erratum in: Bioinformatics. 2021 Apr 1;36(22-23):5562. PMID: 32399560; PMCID: PMC7750954.

  • AMRFinderPlus

    Feldgarden M, Brover V, Gonzalez-Escalona N, Frye JG, Haendiges J, Haft DH, Hoffmann M, Pettengill JB, Prasad AB, Tillman GE, Tyson GH, Klimke W. AMRFinderPlus and the Reference Gene Catalog facilitate examination of the genomic links among antimicrobial resistance, stress response, and virulence. Sci Rep. 2021 Jun 16;11(1):12728. doi: 10.1038/s41598-021-91456-0. PMID: 34135355; PMCID: PMC8208984.

  • DefenseFinder

    Tesson F, Hervé A, Mordret E, Touchon M, d'Humières C, Cury J, Bernheim A. Systematic and quantitative view of the antiviral arsenal of prokaryotes. Nat Commun. 2022 May 10;13(1):2561. doi: 10.1038/s41467-022-30269-9. PMID: 35538097; PMCID: PMC9090908.

  • GECCO

    Carroll LM, Larralde M, Fleck JS, Ponnudurai R, Milanese A, Barazzone EC, Zeller G. Accurate de novo identification of biosynthetic gene clusters with GECCO. bioRxiv 2021.05.03.442509; doi:10.1101/2021.05.03.442509

  • antiSMASH

    Blin K, Shaw S, Augustijn HE, Reitz ZL, Biermann F, Alanjary M, Fetter A, Terlouw BR, Metcalf WW, Helfrich EJN, van Wezel GP, Medema MH, Weber T. antiSMASH 7.0: new and improved predictions for detection, regulation, chemical structures and visualisation. Nucleic Acids Res. 2023 Jul 5;51(W1):W46-W50. doi: 10.1093/nar/gkad344. PMID: 37140036; PMCID: PMC10320115.

  • SanntiS

    Sanchez S, Rogers JD, Rogers AB, Nassar M, McEntyre J, Welch M, Hollfelder F, Finn RD. Expansion of novel biosynthetic gene clusters from diverse environments using SanntiS. bioRxiv 2023.05.23.540769; doi: https://doi.org/10.1101/2023.05.23.540769

  • Pseudofinder

    Syberg-Olsen MJ, Garber AI, Keeling PJ, McCutcheon JP, Husnik F. Pseudofinder: Detection of Pseudogenes in Prokaryotic Genomes. Mol Biol Evol. 2022 Jul 2;39(7):msac153. doi: 10.1093/molbev/msac153. PMID: 35801562; PMCID: PMC9336565.

  • run_dbCAN

    Zheng J, Ge Q, Yan Y, Zhang X, Huang L, Yin Y. dbCAN3: automated carbohydrate-active enzyme and substrate annotation. Nucleic Acids Res. 2023 Jul 5;51(W1):W115-W121. doi: 10.1093/nar/gkad328. PMID: 37125649; PMCID: PMC10320055.

  • CRISPRCasFinder

    Couvin D, Bernheim A, Toffano-Nioche C, Touchon M, Michalik J, Néron B, Rocha EPC, Vergnaud G, Gautheret D, Pourcel C. CRISPRCasFinder, an update of CRISRFinder, includes a portable version, enhanced performance and integrates search for Cas proteins. Nucleic Acids Res. 2018 Jul 2;46(W1):W246-W251. doi: 10.1093/nar/gky425. PMID: 29790974; PMCID: PMC6030898.

  • Infernal

    Nawrocki EP, Eddy SR. Infernal 1.1: 100-fold faster RNA homology searches. Bioinformatics. 2013 Nov 15;29(22):2933-5. doi: 10.1093/bioinformatics/btt509. Epub 2013 Sep 4. PMID: 24008419; PMCID: PMC3810854.

  • Rfam

    Kalvari I, Argasinska J, Quinones-Olvera N, Nawrocki EP, Rivas E, Eddy SR, Bateman A, Finn RD, Petrov AI. Rfam 13.0: shifting to a genome-centric resource for non-coding RNA families. Nucleic Acids Res. 2018 Jan 4;46(D1):D335-D342. doi: 10.1093/nar/gkx1038. PMID: 29112718; PMCID: PMC5753348.

  • tRNAscan-SE

    Chan PP, Lin BY, Mak AJ, Lowe TM. tRNAscan-SE 2.0: improved detection and functional classification of transfer RNA genes. Nucleic Acids Res. 2021 Sep 20;49(16):9077-9096. doi: 10.1093/nar/gkab688. PMID: 34417604; PMCID: PMC8450103.

Software packaging/containerisation tools

  • Anaconda

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

  • Bioconda

    Grüning B, Dale R, Sjödin A, Chapman BA, Rowe J, Tomkins-Tinch CH, Valieris R, Köster J; Bioconda Team. Bioconda: sustainable and comprehensive software distribution for the life sciences. Nat Methods. 2018 Jul;15(7):475-476. doi: 10.1038/s41592-018-0046-7. PubMed PMID: 29967506.

  • BioContainers

    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

    Merkel, D. (2014). Docker: lightweight linux containers for consistent development and deployment. Linux Journal, 2014(239), 2. doi: 10.5555/2600239.2600241.

  • Singularity

    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.