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To cite MIRA-NF

citEntry(
  entry    = "manual",
  title    = "MIRA-NF: A Nextflow Pipeline for Influenza, SARS-CoV-2 and RSV Assembly and Curation",
  author   = "Amanda Sullivan, Kristine Lacek, Reina Chau, Sam Wiley and Ben Rambo-Martin",
  institution = "Centers for Disease Control and Prevention",
  address  = "1600 Clifton Road NE, Building 21, 8th Floor, Atlanta, Georgia 30333",
  year     = "2024",
  textVersion = paste(
  "Sullivan, A. H., Lacek, K., Chau, R., Wiley, S. & Rambo-Martin, B. MIRA-NF: A Nextflow Pipeline for Influenza, SARS-CoV-2 and RSV Assembly and Curation."
  )
)

cdcgov/MIRA-NF: Citations

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

  • FastQC

    Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online].

  • 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.

  • IRMA

Shepard, S.S., Meno, S., Bahl, J. et al. Viral deep sequencing needs an adaptive approach: IRMA, the iterative refinement meta-assembler. BMC Genomics 17, 708 (2016). https://doi.org/10.1186/s12864-016-3030-6

Shepard, S.S., Chettleburgh, W., Wiley, S. IRMA-core: a tool for IRMA and to assist the sequencing of virus genomes. (2025)

Sullivan, A.H., Rambo-Martin, B., Wiley, S., Shepard, S.S. mira-oxide: A set of rusty tools for use in MIRA. (2025)

Aksamentov, I., Roemer, C., Hodcroft, E. B., & Neher, R. A., (2021). Nextclade: clade assignment, mutation calling and quality control for viral genomes. Journal of Open Source Software, 6(67), 3773, https://doi.org/10.21105/joss.03773

Software packaging/containerisation tools

  • 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.