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@article{DiTommaso:2017,
  title = {Nextflow Enables Reproducible Computational Workflows},
  author = {Di Tommaso, Paolo and Chatzou, Maria and Floden, Evan W and Barja, Pablo Prieto and Palumbo, Emilio and Notredame, Cedric},
  date = {2017-04},
  journaltitle = {Nature Biotechnology},
  volume = {35},
  number = {4},
  pages = {316--319},
  doi = {10.1038/nbt.3820}
}


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	title = {Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities},
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	number = {23},
	pages = {7537--7541},
	year = {2009},
	doi = {10.1128/AEM.01541-09},
	issn = {0099-2240},
	URL = {https://aem.asm.org/content/75/23/7537},
	journal = {Applied and Environmental Microbiology}
}

@article{Bolyen:2019,
  title={Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2},
  author={Bolyen, Evan and Rideout, Jai Ram and Dillon, Matthew R and Bokulich, Nicholas A and Abnet, Christian C and Al-Ghalith, Gabriel A and Alexander, Harriet and Alm, Eric J and Arumugam, Manimozhiyan and Asnicar, Francesco and others},
  journal={Nature biotechnology},
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}

@article{Edgar:2016,
  title={UNOISE2: improved error-correction for Illumina 16S and ITS amplicon reads},
  author={Edgar, Robert C and QIIME, Development Team},
  journal={bioRxiv},
  pages={081257},
  year={2016},
  doi = {10.1101/081257}
}

@article{Rognes:2016,
  title={VSEARCH: a versatile open source tool for metagenomics},
  author={Rognes T, Flouri T, Nichols B, Quince C, Mahé F},
  journal={PeerJ},
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  pages={e2584},
  year={2016},
  doi = {10.7717/peerj.2584}
}

@ARTICLE{Martin:2011,
  author = {Marcel Martin},
  title = {Cutadapt removes adapter sequences from high-throughput sequencing reads},
  journal = {EMBnet.journal},
  year = 2011,
  volume = 17,
  pages = {10--12},
  number = 1,
  doi = {10.14806/ej.17.1.200}
}

@article{Zhang:2014,
  title={PEAR: a fast and accurate Illumina Paired-End reAd mergeR},
  author={Zhang, Junying and Kobert, K and Flouri, T and Stamatakis, Alexandros},
  journal={Bioinformatics},
  volume={30},
  number={5},
  pages={614--620},
  year={2014},
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@article{Ewels:2016,
    author = {Ewels, Philip and Magnusson, Måns and Lundin, Sverker and Käller, Max},
    title = "{MultiQC: summarize analysis results for multiple tools and samples in a single report}",
    journal = {Bioinformatics},
    volume = {32},
    number = {19},
    pages = {3047-3048},
    year = {2016},
    month = {06},
    abstract = "{Motivation: Fast and accurate quality control is essential for studies involving next-generation sequencing data. Whilst numerous tools exist to quantify QC metrics, there is no common approach to flexibly integrate these across tools and large sample sets. Assessing analysis results across an entire project can be time consuming and error prone; batch effects and outlier samples can easily be missed in the early stages of analysis.Results: We present MultiQC, a tool to create a single report visualising output from multiple tools across many samples, enabling global trends and biases to be quickly identified. MultiQC can plot data from many common bioinformatics tools and is built to allow easy extension and customization.Availability and implementation: MultiQC is available with an GNU GPLv3 license on GitHub, the Python Package Index and Bioconda. Documentation and example reports are available at http://multiqc.infoContact:  phil.ewels@scilifelab.se}",
    issn = {1367-4803},
    doi = {10.1093/bioinformatics/btw354}
}

@misc{Andrews:2010,
  address = {{Babraham, UK}},
  title = {{{FastQC}}},
  copyright = {GPL v3},
  abstract = {FastQC aims to provide a simple way to do some quality control checks on raw sequence data coming from high throughput sequencing pipelines. It provides a modular set of analyses which you can use to give a quick impression of whether your data has any problems of which you should be aware before doing any further analysis.},
  howpublished = {Babraham Institute},
  author = {Andrews, Simon and Krueger, Felix and {Segonds-Pichon}, Anne and Biggins, Laura and Krueger, Christel and Wingett, Steven},
  month = jan,
  year = {2010}
}