# nf-core/mag: 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

- [BBnorm/BBTools](http://sourceforge.net/projects/bbmap/)

- [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.

- [Centrifuge](https://doi.org/10.1101/gr.210641.116)

  > Kim, D., Song, L., Breitwieser, F. P., & Salzberg, S. L. (2016). Centrifuge: rapid and sensitive classification of metagenomic sequences. Genome research, 26(12), 1721-1729. doi: 10.1101/gr.210641.116.

- [CheckM](https://doi.org/10.1101/gr.186072.114)

  > Parks, D. H., Imelfort, M., Skennerton, C. T., Hugenholtz, P., & Tyson, G. W. (2015). CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Research, 25(7), 1043–1055. doi: 10.1101/gr.186072.114

- [CheckM2](https://doi.org/10.1038/s41592-023-01940-w)

  > Chklovski, A., Parks, D. H., Woodcroft, B. J., & Tyson, G. W. (2023). CheckM2: a rapid, scalable and accurate tool for assessing microbial genome quality using machine learning. Nature Methods, 20(8), 1203-1212. doi: https://doi.org/10.1038/s41592-023-01940-w

- [Chopper](https://doi.org/10.1093/bioinformatics/bty149)

  > De Coster W, D'Hert S, Schultz DT, Cruts M, Van Broeckhoven C. NanoPack: visualizing and processing long-read sequencing data. Bioinformatics. 2018 Aug 1;34(15):2666-2669. doi: 10.1093/bioinformatics/bty149

- [CONCOCT](https://doi.org/10.1038/nmeth.3103)

  > Alneberg, J., Bjarnason, B. S., de Bruijn, I., Schirmer, M., Quick, J., Ijaz, U. Z., Lahti, L., Loman, N. J., Andersson, A. F., & Quince, C. (2014). Binning metagenomic contigs by coverage and composition. Nature Methods, 11(11), 1144–1146. doi: 10.1038/nmeth.3103

- [DAS Tool](https://doi.org/10.1038/s41564-018-0171-1)

  > Sieber, C. M. K., et al. 2018. "Recovery of Genomes from Metagenomes via a Dereplication, Aggregation and Scoring Strategy." Nature Microbiology 3 (7): 836-43. doi: 10.1038/s41564-018-0171-1

- [FastP](https://doi.org/10.1093/bioinformatics/bty560)

  > Chen, S., Zhou, Y., Chen, Y., & Gu, J. (2018). fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics , 34(17), i884–i890. doi: 10.1093/bioinformatics/bty560.

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

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

- [Filtlong](https://github.com/rrwick/Filtlong)

- [Freebayes](https://arxiv.org/abs/1207.3907)

  > Garrison E, Marth G. Haplotype-based variant detection from short-read sequencing. arXiv preprint arXiv:1207.3907 [q-bio.GN] 2012

- [geNomad](https://doi.org/10.1101/2023.03.05.531206)

  > Camargo, A. P., et al. (2023). You can move, but you can’t hide: identification of mobile genetic elements with geNomad. bioRxiv preprint. doi: 10.1101/2023.03.05.531206

- [GTDB-Tk](https://doi.org/10.1093/bioinformatics/btz848)

  > Chaumeil, P. A., Mussig, A. J., Hugenholtz, P., & Parks, D. H. (2020). GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database. Bioinformatics , 36(6), 1925–1927. doi: 10.1093/bioinformatics/btz848.

- [GUNC](https://doi.org/10.1186/s13059-021-02393-0.)

  > Orakov, A., Fullam, A., Coelho, A. P., Khedkar, S., Szklarczyk, D., Mende, D. R., Schmidt, T. S. B., and Bork, P.. 2021. “GUNC: Detection of Chimerism and Contamination in Prokaryotic Genomes.” Genome Biology 22 (1): 178. doi: 10.1186/s13059-021-02393-0.

- [Kraken2](https://doi.org/10.1186/s13059-019-1891-0)

  > Wood, D et al., 2019. Improved metagenomic analysis with Kraken 2. Genome Biology volume 20, Article number: 257. doi: 10.1186/s13059-019-1891-0.

- [Krona](https://doi.org/10.1186/1471-2105-12-385)

  > Ondov, B. D., Bergman, N. H., & Phillippy, A. M. (2011). Interactive metagenomic visualization in a Web browser. BMC bioinformatics, 12(1), 1-10. doi: 10.1186/1471-2105-12-385.

- [MaxBin2](https://doi.org/10.1093/bioinformatics/btv638)

  > Yu-Wei, W., Simmons, B. A. & Singer, S. W. (2015) MaxBin 2.0: An Automated Binning Algorithm to Recover Genomes from Multiple Metagenomic Datasets. Bioinformatics 32 (4): 605–7. doi: 10.1093/bioinformatics/btv638.

- [MEGAHIT](https://doi.org/10.1016/j.ymeth.2016.02.020)

  > Li, D., Luo, R., Liu, C. M., Leung, C. M., Ting, H. F., Sadakane, K., ... & Lam, T. W. (2016). MEGAHIT v1. 0: a fast and scalable metagenome assembler driven by advanced methodologies and community practices. Methods, 102, 3-11. doi: 10.1016/j.ymeth.2016.02.020.

- [MetaBAT2](https://doi.org/10.7717/peerj.7359)

  > Kang, D. D., Li, F., Kirton, E., Thomas, A., Egan, R., An, H., & Wang, Z. (2019). MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies. PeerJ, 7, e7359. doi: 10.7717/peerj.7359.

- [MetaEuk](https://doi.org/10.1186/s40168-020-00808-x)

  > Levy Karin, E., Mirdita, M. & Söding, J. MetaEuk—sensitive, high-throughput gene discovery, and annotation for large-scale eukaryotic metagenomics. Microbiome 8, 48 (2020). 10.1186/s40168-020-00808-x

- [MMseqs2](https://www.nature.com/articles/nbt.3988)

  > Steinegger, M., Söding, J. MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets. Nat Biotechnol 35, 1026–1028 (2017).10.1038/nbt.3988

- [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.

- [NanoLyse](https://doi.org/10.1093/bioinformatics/bty149)

  > De Coster, W., D’Hert, S., Schultz, D. T., Cruts, M., & Van Broeckhoven, C. (2018). NanoPack: visualizing and processing long-read sequencing data. Bioinformatics, 34(15), 2666-2669. doi: 10.1093/bioinformatics/bty149.

- [NanoPlot](https://doi.org/10.1093/bioinformatics/bty149)

  > De Coster, W., D’Hert, S., Schultz, D. T., Cruts, M., & Van Broeckhoven, C. (2018). NanoPack: visualizing and processing long-read sequencing data. Bioinformatics, 34(15), 2666-2669. doi: 10.1093/bioinformatics/bty149.

- [Nanoq](https://doi.org/10.21105/joss.02991)

  > Steinig, E., Coin, L. (2022). Nanoq: ultra-fast quality control for nanopore reads. Journal of Open Source Software, 7(69), 2991, doi: 10.21105/joss.02991

- [Porechop](https://github.com/rrwick/Porechop)

- [Porechop-abi](https://github.com/bonsai-team/Porechop_ABI)

  > Bonenfant, Q., Noé, L., & Touzet, H. (2022). Porechop_ABI: discovering unknown adapters in ONT sequencing reads for downstream trimming. bioRxiv. 10.1101/2022.07.07.499093

- [Prodigal](https://pubmed.ncbi.nlm.nih.gov/20211023/)

  > Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW, Hauser LJ. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics. 2010 Mar 8;11:119. doi: 10.1186/1471-2105-11-119. PMID: 20211023; PMCID: PMC2848648.

- [Prokka](https://pubmed.ncbi.nlm.nih.gov/24642063/)

  > 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.

- [PyDamage](https://doi.org/10.7717/peerj.11845)

  > Borry M, Hübner A, Rohrlach AB, Warinner C. 2021. PyDamage: automated ancient damage identification and estimation for contigs in ancient DNA de novo assembly. PeerJ 9:e11845 doi: 10.7717/peerj.11845

- [SAMtools](https://doi.org/10.1093/bioinformatics/btp352)

  > Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., … 1000 Genome Project Data Processing Subgroup. (2009). The Sequence Alignment/Map format and SAMtools. Bioinformatics , 25(16), 2078–2079. doi: 10.1093/bioinformatics/btp352.

- [Seqtk](https://github.com/lh3/seqtk)

- [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.

- [Tiara](https://doi.org/10.1093/bioinformatics/btab672)

  > Karlicki, M., Antonowicz, S., Karnkowska, A., 2022. Tiara: deep learning-based classification system for eukaryotic sequences. Bioinformatics 38, 344–350. doi: 10.1093/bioinformatics/btab672

## Data

- [Full-size test data](https://doi.org/10.1038/s41587-019-0191-2)

  > Bertrand, D., Shaw, J., Kalathiyappan, M., Ng, A. H. Q., Kumar, M. S., Li, C., ... & Nagarajan, N. (2019). Hybrid metagenomic assembly enables high-resolution analysis of resistance determinants and mobile elements in human microbiomes. Nature biotechnology, 37(8), 937-944. doi: 10.1038/s41587-019-0191-2.

## 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 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](https://pubmed.ncbi.nlm.nih.gov/28379341/)

  > 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](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.
