# References and external links

This pipeline uses several tools and external ressources. 
Documentation for these can be found at the links below:

| Tool | Link |
| --- | --- |
| BLAST | [https://blast.ncbi.nlm.nih.gov/Blast.cgi](https://blast.ncbi.nlm.nih.gov/Blast.cgi) |
| Conda | [https://docs.conda.io/en/latest/](https://docs.conda.io/en/latest/) |
| Cutadapt | [https://cutadapt.readthedocs.io/en/stable/](https://cutadapt.readthedocs.io/en/stable/) |
| create_sampleSheet | [https://gitlab.com/bfr_bioinformatics/AQUAMIS](https://gitlab.com/bfr_bioinformatics/AQUAMIS) |
| DADA2 | [https://benjjneb.github.io/dada2/](https://benjjneb.github.io/dada2/) |
| DT | [https://rstudio.github.io/DT/](https://rstudio.github.io/DT/) |
| fastp | [https://github.com/OpenGene/fastp](https://github.com/OpenGene/fastp) |
| Krona | [https://bio.tools/krona](https://bio.tools/krona) |
| Pandas | [https://pandas.pydata.org/](https://pandas.pydata.org/) |
| RMarkdown | [https://rmarkdown.rstudio.com/](https://rmarkdown.rstudio.com/) |
| SeqTK | [https://github.com/lh3/seqtk](https://github.com/lh3/seqtk) |
| Snakemake | [https://snakemake.readthedocs.io/en/stable/](https://snakemake.readthedocs.io/en/stable/) |
| scikit-learn | [https://scikit-learn.org/stable/](https://scikit-learn.org/stable/)
| taxidTools | [https://cvua-rrw.github.io/taxidTools/](https://cvua-rrw.github.io/taxidTools/) |
| Tidyverse | [https://www.tidyverse.org/](https://www.tidyverse.org/) |
| VSEARCH | [https://github.com/torognes/vsearch](https://github.com/torognes/vsearch) |

