Citations
TwistMethylFlow
Das, J. (2024). TwistMethylFlow (v1.0.0). Zenodo. https://doi.org/10.5281/zenodo.14204261
Pipeline tools
FastQC
Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online].
Trim Galore
Felix Krueger, Frankie James, Phil Ewels, Ebrahim Afyounian, Michael Weinstein, Benjamin Schuster-Boeckler, Gert Hulselmans, & sclamons. (2023). FelixKrueger/TrimGalore: v0.6.10 - add default decompression path (0.6.10). Zenodo. https://doi.org/10.5281/zenodo.7598955
Bismark
Krueger, F., & Davies, R. (2019). Bismark: a versatile tool for aligning sequencing data to bisulfite-converted genomes. Bioinformatics, 35(4), 623-625. https://doi.org/10.1093/bioinformatics/bty724
SAMtools
Danecek P, Bonfield JK, Liddle J, et al. Twelve years of SAMtools and BCFtools. GigaScience. 2021;10(2):giab008. doi:10.1093/gigascience/giab008
QualiMap
Konstantin Okonechnikov, Ana Conesa, Fernando García-Alcalde, Qualimap 2: advanced multi-sample quality control for high-throughput sequencing data, Bioinformatics, Volume 32, Issue 2, January 2016, Pages 292–294, https://doi.org/10.1093/bioinformatics/btv566
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.
EdgeR
Chen Y, Chen L, Lun ATL, Baldoni P, Smyth GK (2025). “edgeR v4: powerful differential analysis of sequencing data with expanded functionality and improved support for small counts and larger datasets.” Nucleic Acids Research, 53(2), gkaf018. doi:10.1093/nar/gkaf018.
MethylKit
Morgan, M., & Huber, W. (2020). methylKit: a package for the analysis of DNA methylation data in R. Bioinformatics, 36(1), 214-216. https://doi.org/10.1093/bioinformatics/btz262
ggplot2
Wickham H (2016). ggplot2: Elegant Graphics for Data Analysis. Springer-Verlag New York. ISBN 978-3-319-24277-4, https://ggplot2.tidyverse.org.
Gene Ontology
Xu S, Hu E, Cai Y, Xie Z, Luo X, Zhan L, Tang W, Wang Q, Liu B, Wang R, Xie W, Wu T, Xie L, Yu G (2024). “Using clusterProfiler to characterize multiomics data.” Nature Protocols, 19(11), 3292-3320. doi:10.1038/s41596-024-01020-z, https://www.nature.com/articles/s41596-024-01020-z.
Walter, Wencke, Fátima Sánchez-Cabo, and Mercedes Ricote. "GOplot: an R package for visually combining expression data with functional analysis." Bioinformatics (2015): btv300.
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
Merkel, D. (2014). Docker: lightweight linux containers for consistent development and deployment. Linux Journal, 2014(239), 2. doi: 10.5555/2600239.2600241.
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.
R and Bioconductor
R. Ihaka and R. Gentleman (1996), R: A Language for Data Analysis and Graphics, Journal of Computational and Graphical Statistics, Vol 5, No 3, 299-314.
Huber, W., Carey, V., Gentleman, R. et al. Orchestrating high-throughput genomic analysis with Bioconductor. Nat Methods 12, 115–121 (2015). https://doi.org/10.1038/nmeth.3252.
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.
📄 Citation
If you use TwistMethylFlow in your work, please cite:
Das, J. (2024). TwistMethylFlow (v1.0.0). Zenodo. https://doi.org/10.5281/zenodo.14204261
📜 License
This project is licensed under the terms of the GNU General Public License v3.0.
🙏 Acknowledgements
Research Institutions
Core Facility, Faculty of Medicine and Health Sciences, Linköping University Linköping University Core Facility
Clinical Genomics Linköping, Science for Life Laboratory, Sweden Clinical Genomics Linköping
National Academic Infrastructure for Supercomputing in Sweden (NAISS)
The computations/data storage were enabled by resources provided by the National Academic Infrastructure for Supercomputing in Sweden (NAISS), partially funded by the Swedish Research Council through grant agreement no. 2022-06725.
These institutions provided invaluable resources and support for the development and testing of the TwistMethylFlow pipeline.
Additional Thanks
Users and Testers: A heartfelt thank you to all the early adopters, testers, and collaborators who helped refine and improve the tool through their feedback and bug reports.
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