taxprofiler/CITATIONS.md

# nf-core/taxprofiler: 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

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

- [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.

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

  > Chen, Shifu, Yanqing Zhou, Yaru Chen, and Jia Gu. 2018. Fastp: An Ultra-Fast All-in-One FASTQ Preprocessor. Bioinformatics 34 (17): i884-90. 10.1093/bioinformatics/bty560.

- [AdapterRemoval2](https://doi.org/10.1186/s13104-016-1900-2)

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

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

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

- [PRINSEQ++](https://doi.org/10.7287/peerj.preprints.27553v1)

  > Cantu, Vito Adrian, Jeffrey Sadural, and Robert Edwards. 2019. PRINSEQ++, a Multi-Threaded Tool for Fast and Efficient Quality Control and Preprocessing of Sequencing Datasets. e27553v1. PeerJ Preprints. doi: 10.7287/peerj.preprints.27553v1.

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

  > Wood, Derrick E., Jennifer Lu, and Ben Langmead. 2019. Improved Metagenomic Analysis with Kraken 2. Genome Biology 20 (1): 257. doi: 10.1186/s13059-019-1891-0.

- [KrakenUniq](https://doi.org/10.1186/s13059-018-1568-0)

  > Breitwieser, Florian P., Daniel N. Baker, and Steven L. Salzberg. 2018. KrakenUniq: confident and fast metagenomics classification using unique k-mer counts. Genome Biology 19 (1): 198. doi: 10.1186/s13059-018-1568-0

- [Bracken](https://doi.org/10.7717/peerj-cs.104)

  > Lu, J., Breitwieser, F. P., Thielen, P., & Salzberg, S. L. (2017). Bracken: Estimating species abundance in metagenomics data. PeerJ Computer Science, 3, e104. doi: 10.7717/peerj-cs.104

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

  > Ondov, Brian D., Nicholas H. Bergman, and Adam M. Phillippy. 2011. Interactive metagenomic visualization in a Web browser. BMC Bioinformatics 12 (1): 385. doi: 10.1186/1471-2105-12-385.

- [MALT](https://doi.org/10.1038/s41559-017-0446-6)

  > Vågene, Åshild J., Alexander Herbig, Michael G. Campana, Nelly M. Robles García, Christina Warinner, Susanna Sabin, Maria A. Spyrou, et al. 2018. Salmonella Enterica Genomes from Victims of a Major Sixteenth-Century Epidemic in Mexico. Nature Ecology & Evolution 2 (3): 520-28. doi: 10.1038/s41559-017-0446-6.

- [MEGAN](https://doi.org/10.1371/journal.pcbi.1004957)

  > Huson, Daniel H., Sina Beier, Isabell Flade, Anna Górska, Mohamed El-Hadidi, Suparna Mitra, Hans-Joachim Ruscheweyh, and Rewati Tappu. 2016. “MEGAN Community Edition - Interactive Exploration and Analysis of Large-Scale Microbiome Sequencing Data.” PLoS Computational Biology 12 (6): e1004957. doi: 10.1371/journal.pcbi.1004957.

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

  > Beghini, Francesco, Lauren J McIver, Aitor Blanco-Míguez, Leonard Dubois, Francesco Asnicar, Sagun Maharjan, Ana Mailyan, et al. 2021. “Integrating Taxonomic, Functional, and Strain-Level Profiling of Diverse Microbial Communities with BioBakery 3.” Edited by Peter Turnbaugh, Eduardo Franco, and C Titus Brown. ELife 10 (May): e65088. doi: 10.7554/eLife.65088

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

  > Kim, Daehwan, Li Song, Florian P. Breitwieser, and Steven L. Salzberg. 2016. “Centrifuge: Rapid and Sensitive Classification of Metagenomic Sequences.” Genome Research 26 (12): 1721-29. doi: 10.1101/gr.210641.116.

- [DIAMOND](https://doi.org/10.1038/nmeth.3176)

> Buchfink, Benjamin, Chao Xie, and Daniel H. Huson. 2015. “Fast and Sensitive Protein Alignment Using DIAMOND.” Nature Methods 12 (1): 59-60. doi: 10.1038/nmeth.3176.

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

- [falco](https://doi.org/10.12688/f1000research.21142.2)

> de Sena Brandine G and Smith AD. Falco: high-speed FastQC emulation for quality control of sequencing data. F1000Research 2021, 8:1874

## 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)

- [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.
initial template build from nf-core/tools, version 2.2 2022-02-18 06:55:14 +00:00			`# nf-core/taxprofiler: 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`

Template update for nf-core/tools version 2.3.1 2022-03-23 13:57:56 +00:00			`- [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)`
initial template build from nf-core/tools, version 2.2 2022-02-18 06:55:14 +00:00
Template update for nf-core/tools version 2.3.1 2022-03-23 13:57:56 +00:00			`- [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/)`
Prettier linting 2022-04-01 09:13:36 +00:00
Template update for nf-core/tools version 2.3.1 2022-03-23 13:57:56 +00:00			`> 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.`
initial template build from nf-core/tools, version 2.2 2022-02-18 06:55:14 +00:00
Prettier linting 2022-04-01 09:13:36 +00:00			`- [fastp](https://doi.org/10.1093/bioinformatics/bty560)`

Add prinseq as alternative complexity filtering 2022-04-04 19:16:51 +00:00			`> Chen, Shifu, Yanqing Zhou, Yaru Chen, and Jia Gu. 2018. Fastp: An Ultra-Fast All-in-One FASTQ Preprocessor. Bioinformatics 34 (17): i884-90. 10.1093/bioinformatics/bty560.`
Prettier linting 2022-04-01 09:13:36 +00:00
			`- [AdapterRemoval2](https://doi.org/10.1186/s13104-016-1900-2)`

Add prinseq as alternative complexity filtering 2022-04-04 19:16:51 +00:00			`> Schubert, Mikkel, Stinus Lindgreen, and Ludovic Orlando. 2016. AdapterRemoval v2: Rapid Adapter Trimming, Identification, and Read Merging. BMC Research Notes 9 (February): 88. doi:10.1186/s13104-016-1900-2.`
Prettier linting 2022-04-01 09:13:36 +00:00
			`- [Porechop](https://github.com/rrwick/Porechop)`

Add bbduk complexity (entropy-based) filtering 2022-04-02 15:02:05 +00:00			`- [BBTools](http://sourceforge.net/projects/bbmap/)`

Add prinseq as alternative complexity filtering 2022-04-04 19:16:51 +00:00			`- [PRINSEQ++](https://doi.org/10.7287/peerj.preprints.27553v1)`

			`> Cantu, Vito Adrian, Jeffrey Sadural, and Robert Edwards. 2019. PRINSEQ++, a Multi-Threaded Tool for Fast and Efficient Quality Control and Preprocessing of Sequencing Datasets. e27553v1. PeerJ Preprints. doi: 10.7287/peerj.preprints.27553v1.`

Prettier linting 2022-04-01 09:13:36 +00:00			`- [Kraken2](https://doi.org/10.1186/s13059-019-1891-0)`

Add prinseq as alternative complexity filtering 2022-04-04 19:16:51 +00:00			`> Wood, Derrick E., Jennifer Lu, and Ben Langmead. 2019. Improved Metagenomic Analysis with Kraken 2. Genome Biology 20 (1): 257. doi: 10.1186/s13059-019-1891-0.`
Prettier linting 2022-04-01 09:13:36 +00:00
Update documentation for krakenuniq 2022-10-31 16:41:35 +00:00			`- [KrakenUniq](https://doi.org/10.1186/s13059-018-1568-0)`

			`> Breitwieser, Florian P., Daniel N. Baker, and Steven L. Salzberg. 2018. KrakenUniq: confident and fast metagenomics classification using unique k-mer counts. Genome Biology 19 (1): 198. doi: 10.1186/s13059-018-1568-0`

docs: add Bracken reference 2022-10-27 08:14:57 +00:00			`- [Bracken](https://doi.org/10.7717/peerj-cs.104)`

			`> Lu, J., Breitwieser, F. P., Thielen, P., & Salzberg, S. L. (2017). Bracken: Estimating species abundance in metagenomics data. PeerJ Computer Science, 3, e104. doi: 10.7717/peerj-cs.104`

Add citation for Krona 2022-06-14 15:54:10 +00:00			`- [Krona](https://doi.org/10.1186/1471-2105-12-385)`

			`> Ondov, Brian D., Nicholas H. Bergman, and Adam M. Phillippy. 2011. Interactive metagenomic visualization in a Web browser. BMC Bioinformatics 12 (1): 385. doi: 10.1186/1471-2105-12-385.`

Prettier linting 2022-04-01 09:13:36 +00:00			`- [MALT](https://doi.org/10.1038/s41559-017-0446-6)`
More linting 2022-04-01 09:13:57 +00:00
Add prinseq as alternative complexity filtering 2022-04-04 19:16:51 +00:00			`> Vågene, Åshild J., Alexander Herbig, Michael G. Campana, Nelly M. Robles García, Christina Warinner, Susanna Sabin, Maria A. Spyrou, et al. 2018. Salmonella Enterica Genomes from Victims of a Major Sixteenth-Century Epidemic in Mexico. Nature Ecology & Evolution 2 (3): 520-28. doi: 10.1038/s41559-017-0446-6.`
Add Porechop 2022-03-18 14:46:03 +00:00
Add generation of taxon-table like output for MALT 2022-04-16 05:42:30 +00:00			`- [MEGAN](https://doi.org/10.1371/journal.pcbi.1004957)`

			`> Huson, Daniel H., Sina Beier, Isabell Flade, Anna Górska, Mohamed El-Hadidi, Suparna Mitra, Hans-Joachim Ruscheweyh, and Rewati Tappu. 2016. “MEGAN Community Edition - Interactive Exploration and Analysis of Large-Scale Microbiome Sequencing Data.” PLoS Computational Biology 12 (6): e1004957. doi: 10.1371/journal.pcbi.1004957.`

chore: add citation 2022-04-02 11:59:10 +00:00			`- [MetaPhlAn3](https://doi.org/10.7554/eLife.65088)`

Add generation of taxon-table like output for MALT 2022-04-16 05:42:30 +00:00			`> Beghini, Francesco, Lauren J McIver, Aitor Blanco-Míguez, Leonard Dubois, Francesco Asnicar, Sagun Maharjan, Ana Mailyan, et al. 2021. “Integrating Taxonomic, Functional, and Strain-Level Profiling of Diverse Microbial Communities with BioBakery 3.” Edited by Peter Turnbaugh, Eduardo Franco, and C Titus Brown. ELife 10 (May): e65088. doi: 10.7554/eLife.65088`

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

			`> Kim, Daehwan, Li Song, Florian P. Breitwieser, and Steven L. Salzberg. 2016. “Centrifuge: Rapid and Sensitive Classification of Metagenomic Sequences.” Genome Research 26 (12): 1721-29. doi: 10.1101/gr.210641.116.`
chore: add citation 2022-04-02 11:59:10 +00:00
Add draft version of DIAMOND 2022-04-29 19:59:42 +00:00			`- [DIAMOND](https://doi.org/10.1038/nmeth.3176)`

			`> Buchfink, Benjamin, Chao Xie, and Daniel H. Huson. 2015. “Fast and Sensitive Protein Alignment Using DIAMOND.” Nature Methods 12 (1): 59-60. doi: 10.1038/nmeth.3176.`

Add initial longread QC filtering - requires filtlong module update 2022-05-01 05:18:14 +00:00			`- [FILTLONG](https://github.com/rrwick/Filtlong)`

Apply review suggestions 2022-10-20 14:55:57 +00:00			`- [falco](https://doi.org/10.12688/f1000research.21142.2)`
Add Falco as an alternative to FastQC 2022-10-18 15:43:16 +00:00
			`> de Sena Brandine G and Smith AD. Falco: high-speed FastQC emulation for quality control of sequencing data. F1000Research 2021, 8:1874`

initial template build from nf-core/tools, version 2.2 2022-02-18 06:55:14 +00:00			`## Software packaging/containerisation tools`

Template update for nf-core/tools version 2.3.1 2022-03-23 13:57:56 +00:00			`- [Anaconda](https://anaconda.com)`
initial template build from nf-core/tools, version 2.2 2022-02-18 06:55:14 +00:00
Template update for nf-core/tools version 2.3.1 2022-03-23 13:57:56 +00:00			`> Anaconda Software Distribution. Computer software. Vers. 2-2.4.0. Anaconda, Nov. 2016. Web.`
initial template build from nf-core/tools, version 2.2 2022-02-18 06:55:14 +00:00
Template update for nf-core/tools version 2.3.1 2022-03-23 13:57:56 +00:00			`- [Bioconda](https://pubmed.ncbi.nlm.nih.gov/29967506/)`
initial template build from nf-core/tools, version 2.2 2022-02-18 06:55:14 +00:00
Template update for nf-core/tools version 2.3.1 2022-03-23 13:57:56 +00:00			`> 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.`
initial template build from nf-core/tools, version 2.2 2022-02-18 06:55:14 +00:00
Template update for nf-core/tools version 2.3.1 2022-03-23 13:57:56 +00:00			`- [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)`

			`- [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.`