Software

The following software packaged were used for processing and analysis:

Software	Citation
Bowtie2	Langmead B, et al., Nat Methods, 2012, DOI: 10.1038/nmeth.1923
Canvas	Chovanec P, et al., Nat Communications, 2021, DOI: 10.1038/s41467-021-22201-4
Chicago	Cairns J, et al., Genome Biology, 2016, DOI: 10.1186/s13059-016-0992-2
FastQC	https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
FastQScreen	Wingett SW, et al., F1000Res, 2018, DOI: 10.12688/f1000research.15931.2
Gephi	Bastian M., Heymann S., Jacomy M. (2009). Gephi: an open source software for exploring and manipulating networks. International AAAI Conference on Weblogs and Social Media.
HICUP	Wingett SW, et al., F1000Res, DOI:10.12688/f1000research.7334.1
Hisat2	Kim D, et al., Nat Biotechnology, 2019, DOI: 10.1038/s41587-019-0201-4
Igraph	Csardi G, Nepusz T (2006). “The igraph software package for complex network research.” InterJournal, Complex Systems, 1695. https://igraph.org.
MultiQC	Ewels P, et al., Bioinformatics, 2016, DOI: 10.1093/bioinformatics/btw354
R	R Core Team (2021). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria.URL https://www.R-project.org/.
Seqmonk	https://www.bioinformatics.babraham.ac.uk/projects/seqmonk/
Tidyverse	Wickham H, et al., Journal of Open Source Software, DOI: 10.21105/joss.01686
Trim Galore	https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/, latest release DOI: 10.5281/zenodo.5127899
Uwot	McInnes L, et al., arXiv, 2018, DOI: 10.48550/arXiv.1802.03426
Weka	Eibe Frank, Mark A. Hall, and Ian H. Witten (2016). The WEKA Workbench. Online Appendix for "Data Mining: Practical Machine Learning Tools and Techniques", Morgan Kaufmann, Fourth Edition, 2016.