Skip to content

Latest commit

 

History

History
105 lines (56 loc) · 6.17 KB

CITATIONS.md

File metadata and controls

105 lines (56 loc) · 6.17 KB

OceanOmics-amplicon-nf: Citations

nf-core

This pipeline uses code and infrastructure developed and maintained by the nf-core initative, and reused here under the MIT license.

The nf-core framework for community-curated bioinformatics pipelines.

Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.

Nat Biotechnol. 2020 Feb 13. doi: 10.1038/s41587-020-0439-x.

In addition, references of tools and data used in this pipeline are as follows:

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

  • AdapterRemoval

    Schubert M, Lindgreen S, Orlando L. AdapterRemoval v2: rapid adapter trimming, identification, and read merging. BMC Res Notes. 2016 Feb 12;9:88. doi: 10.1186/s13104-016-1900-2. PubMed PMID: 26868221; PubMed Central PMCID: PMC4751634.

  • Biostrings

    Pagès H, Aboyoun P, Gentleman R, DebRoy S (2023). Biostrings: Efficient manipulation of biological strings. R package version 2.66.0, https://bioconductor.org/packages/Biostrings.

  • Blast

  • Csvtk

  • Cutadapt

    Martin, M (2011). Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet.journal, 17(1), pp. 10-12. doi:https://doi.org/10.14806/ej.17.1.200

  • DADA2

    Callahan BJ, McMurdie PJ, Rosen MJ, Han AW, Johnson AJA, Holmes SP (2016). “DADA2: High-resolution sample inference from Illumina amplicon data.” Nature Methods, 13, 581-583. doi:10.1038/nmeth.3869.

  • DECIPHER

    Wright ES (2016). “Using DECIPHER v2.0 to Analyze Big Biological Sequence Data in R.” The R Journal, 8(1), 352-359.

  • Fastp

  • FastQC

  • joblib

  • LCA

    Mousavi-Derazmahalleh M, Stott A, Lines R, Peverley G, Nester G, Simpson T, Zawierta M, De La Pierre M, Bunce M, Christophersen CT. eDNAFlow, an automated, reproducible and scalable workflow for analysis of environmental DNA sequences exploiting Nextflow and Singularity. Mol Ecol Resour. 2021 Jul;21(5):1697-1704. doi: 10.1111/1755-0998.13356. Epub 2021 Mar 9. PMID: 33580619.

  • LULU

    Frøslev, T. G., Kjøller, R., Bruun, H. H., Ejrnæs, R., Brunbjerg, A. K., Pietroni, C., & Hansen, A. J. (2017). Algorithm for post-clustering curation of DNA amplicon data yields reliable biodiversity estimates. Nature Communications, 8(1), 1188.

  • Mmv

  • 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.

  • Obitools3

  • Pandas

  • PEAR

    Zhang, J., Kobert, K., Flouri, T., & Stamatakis, A. (2014). PEAR: a fast and accurate Illumina Paired-End reAd mergeR. Bioinformatics (Oxford, England), 30(5), 614–620. https://doi.org/10.1093/bioinformatics/btt593

  • phangorn

  • phyloseq

    McMurdie PJ, Holmes S (2013). “phyloseq: An R package for reproducible interactive analysis and graphics of microbiome census data.” PLoS ONE, 8(4), e61217. http://dx.plos.org/10.1371/journal.pone.0061217.

  • Seqkit

  • Seqtk

  • Usearch

  • Vsearch

    Rognes T, Flouri T, Nichols B, Quince C, Mahé F. VSEARCH: a versatile open source tool for metagenomics. PeerJ. 2016 Oct 18;4:e2584. doi: 10.7717/peerj.2584. PMID: 27781170; PMCID: PMC5075697.

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

  • 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.