# metabiomx: 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

- [AdapterRemoval2](https://doi.org/10.1186/)

  > Schubert, M., Lindgreen, S., and Orlando, L. 2016. "AdapterRemoval v2: Rapid Adapter Trimming, Identification, and Read Merging." BMC Research Notes 9 (February): 88. doi: 10.1186/s13104-016-1900-2

- [Trimmomatic](https://doi.org/10.1093/bioinformatics/btu170)

  > Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014 Aug 1;30(15):2114-20. doi: 10.1093/bioinformatics/btu170. Epub 2014 Apr 1. PMID: 24695404; PMCID: PMC4103590.

- [BBTools](https://doi.org/10.1371/journal.pone.0185056)

  > Bushnell B, Rood J, Singer E (2017) BBMerge – Accurate paired shotgun read merging via overlap. PLOS ONE 12(10): e0185056.

- [BCFtools](https://doi.org/10.1093/gigascience/giab008)

  > Danecek, Petr, et al. "Twelve years of SAMtools and BCFtools." Gigascience 10.2 (2021): giab008. doi: 10.1093/gigascience/giab008

- [Bowtie2](https:/dx.doi.org/10.1038/nmeth.1923)

  > Langmead, B. and Salzberg, S. L. 2012 Fast gapped-read alignment with Bowtie 2. Nature methods, 9(4), p. 357–359. doi: 10.1038/nmeth.1923.

- [Busco](https://doi.org/10.1007/978-1-4939-9173-0_14)

  > Seppey, M., Manni, M., & Zdobnov, E. M. (2019). BUSCO: assessing genome assembly and annotation completeness. In Gene prediction (pp. 227-245). Humana, New York, NY. doi: 10.1007/978-1-4939-9173-0_14.

- [CAT](https://doi.org/10.1186/s13059-019-1817-x)

  > von Meijenfeldt, F. B., Arkhipova, K., Cambuy, D. D., Coutinho, F. H., & Dutilh, B. E. (2019). Robust taxonomic classification of uncharted microbial sequences and bins with CAT and BAT. Genome biology, 20(1), 1-14. doi: 10.1186/s13059-019-1817-x.

- [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)

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

- [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/)

  > 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.

- [SPAdes](https://doi.org/10.1101/gr.213959.116)

  > Nurk, S., Meleshko, D., Korobeynikov, A., & Pevzner, P. A. (2017). metaSPAdes: a new versatile metagenomic assembler. Genome research, 27(5), 824-834. doi: 10.1101/gr.213959.116.

- [MetaPhlAn3/HUMAnN3](https://doi.org/10.7554/eLife.65088)

  > Francesco BeghiniLauren J McIverAitor Blanco-MíguezLeonard DuboisFrancesco AsnicarSagun MaharjanAna MailyanPaolo ManghiMatthias ScholzAndrew Maltez ThomasMireia Valles-ColomerGeorge WeingartYancong ZhangMoreno ZolfoCurtis HuttenhowerEric A FranzosaNicola Segata (2021) Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3 eLife 10:e65088.

- [biom-format](https://doi.org/10.1186/2047-217X-1-7)

  > Daniel McDonald, Jose C Clemente, Justin Kuczynski, Jai Ram Rideout, Jesse Stombaugh, Doug Wendel, Andreas Wilke, Susan Huse, John Hufnagle, Folker Meyer, Rob Knight, J Gregory Caporaso, The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome, GigaScience, Volume 1, Issue 1, December 2012, 2047–217X–1–7, https://doi.org/10.1186/2047-217X-1-7

- [OmicFlow](https://cran.r-project.org/package=OmicFlow)

  > Gusinac A, Ederveen T, Boleij A (2025). OmicFlow: Fast and Efficient (Automated) Analysis of Sparse Omics Data., https://CRAN.R-project.org/package=OmicFlow.

## Software packaging/containerisation tools
- [Docker](https://dl.acm.org/doi/10.5555/2600239.2600241)

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