---
title: 'Short reads evaluation with [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)'
output:
    html_document:
      number_sections: true
      toc: true
      theme: cosmo
      highlight: tango
---

```{r setup, include=FALSE, warning=FALSE, message=FALSE}
knitr::opts_chunk$set(
  echo = as.logical(opt$X_e),
  error = TRUE,
  eval = TRUE
)
```





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### Kmer Content {.tabset}

#### Before

```{r 'Kmer Content (before)', fig.width=10}
kc_1 = extract_data_module(paste0(opt$X_d, '/read_1_fastqc/fastqc_data.txt'), 'Kmer Content')
knitr::kable(kc_1)
```

#### After
```{r 'Kmer Content (after)', fig.width=10}
kc_2 = extract_data_module(paste0(opt$X_d, '/read_2_fastqc/fastqc_data.txt'), 'Kmer Content')
knitr::kable(kc_2)
```


# Session Info

```{r 'session info'}
sessionInfo()
```

# References

* Bioinformatics, Babraham (2014). FastQC.

* Allaire, J and Cheng, Joe and Xie, Yihui and McPherson, Jonathan and Chang, Winston and Allen, Jeff and Wickham, Hadley and Atkins, Aron and Hyndman, Rob (2016). rmarkdown: Dynamic Documents for R, 2016. In R package version 0.9, 6.

* Xie, Yihui (2015). Dynamic Documents with R and knitr, CRC Press, Vol.29.

* Carson Sievert and Chris Parmer and Toby Hocking and Scott Chamberlain and Karthik Ram and Marianne Corvellec and Pedro Despouy (2017). plotly: Create Interactive Web Graphics via 'plotly.js'. R package version 4.6.0. [Link]

* Wickham, H. (2016). ggplot2: elegant graphics for data analysis. Springer. Chicago