Merge pull request #225 from DanielEWeeks/patch-1 #30

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[link text too short]: [R](https://en.wikipedia.org/wiki/R_(programming_language))

[uninformative link text]: [here](https://cran.r-project.org/package=here)

[uninformative link text]: [here](https://www.r-bloggers.com/r-tutorial-on-the-apply-family-of-functions/)

[uninformative link text]: [here](https://swcarpentry.github.io/r-novice-inflammation/15-supp-loops-in-depth/)

[uninformative link text]: [here](https://www.bioconductor.org/install/)

[link text too short]: [r](https://stackoverflow.com/questions/tagged/r)

[uninformative link text]: [Link](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/)

[uninformative link text]: [Link](https://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/TrimmomaticManual_V0.32.pdf)

[uninformative link text]: [Link](https://bio-bwa.sourceforge.net/bwa.shtml)

[uninformative link text]: [Link](https://www.htslib.org/doc/samtools.html)