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CITATIONS.md
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CITATIONS.md
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- [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
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- [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/)
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> Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924.
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* [Porechop](https://github.com/rrwick/Porechop)
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- [fastp](https://doi.org/10.1093/bioinformatics/bty560)
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> Chen, Shifu, Yanqing Zhou, Yaru Chen, and Jia Gu. 2018. “Fastp: An Ultra-Fast All-in-One FASTQ Preprocessor.” Bioinformatics 34 (17): i884-90. 10.1093/bioinformatics/bty560.
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- [AdapterRemoval2](https://doi.org/10.1186/s13104-016-1900-2)
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> Schubert, Mikkel, Stinus Lindgreen, and Ludovic Orlando. 2016. “AdapterRemoval v2: Rapid Adapter Trimming, Identification, and Read Merging.” BMC Research Notes 9 (February): 88. doi:10.1186/s13104-016-1900-2.
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- [Porechop](https://github.com/rrwick/Porechop)
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- [Kraken2](https://doi.org/10.1186/s13059-019-1891-0)
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> Wood, Derrick E., Jennifer Lu, and Ben Langmead. 2019. “Improved Metagenomic Analysis with Kraken 2.” Genome Biology 20 (1): 257. doi: 10.1186/s13059-019-1891-0.
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- [MALT](https://doi.org/10.1038/s41559-017-0446-6)
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> Vågene, Åshild J., Alexander Herbig, Michael G. Campana, Nelly M. Robles García, Christina Warinner, Susanna Sabin, Maria A. Spyrou, et al. 2018. “Salmonella Enterica Genomes from Victims of a Major Sixteenth-Century Epidemic in Mexico.” Nature Ecology & Evolution 2 (3): 520-28. doi: 10.1038/s41559-017-0446-6.
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## Software packaging/containerisation tools
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}
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}
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}
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}
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}
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