References

[1]

Köster, J., Mölder, F., Jablonski, K. P., Letcher, B., Hall, M. B., Tomkins-Tinch, C. H., … Nahnsen, S. (2021). Sustainable data analysis with snakemake. F1000Research, 10. https://doi.org/10.12688/f1000research.29032.2

[2]

SnakeDeploy. Retrieved from https://github.com/snakemake/snakedeploy

[3]

R Core Team. (2021). R: A language and environment for statistical computing. Vienna, Austria: R Foundation for Statistical Computing. Retrieved from https://www.R-project.org/

[4]

RStudio Team. (2021). RStudio: Integrated development environment for r. Boston, MA: RStudio, PBC. Retrieved from http://www.rstudio.com/

[5]

Shen, W., Le, S., Li, Y., & Hu, F. (2016). SeqKit: A cross-platform and ultrafast toolkit for FASTA/q file manipulation. PLoS ONE, 11. https://doi.org/10.1371/JOURNAL.PONE.0163962

[6]

Andrews, S. (2018). FastQC: Https://www.bioinformatics.babraham.ac.uk/projects/fastqc/. Retrieved from https://www.bioinformatics.babraham.ac.uk/projects/fastqc/

[7]

Ewels, P., Magnusson, M., Lundin, S., & Kaller, M. (2016). MultiQC: Summarize analysis results for multiple tools and samples in a single report. Bioinformatics, 32, 3047–3048. https://doi.org/10.1093/bioinformatics/btw354

[8]

Bushnell, B. (2016). BBMap short-read aligner, and other bioinformatics tools. Retrieved from http://sourceforge.net/projects/bbmap/

[9]

Bolger, A. M., Lohse, M., & Usadel, B. (2014). Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics, 30(15), 2114–2120. https://doi.org/10.1093/bioinformatics/btu170

[10]

Biobakery. (2022). Biobakery kneaddata:quality control tool on metagenomic and metatranscriptomic sequencing data. Retrieved from https://github.com/biobakery/kneaddata