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Jordy P. M. Coolen et al.
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Hector F. Espitia-Navarro et al.
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Ruth E. Timme et al.
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Balamurugan Jagadeesan et al.
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Anderson C. Camargo et al.
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Cyril Savin et al.
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Anais Painset et al.
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Susanne Schjorring et al.
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Yi Chen et al.
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MultiQC: summarize analysis results for multiple tools and samples in a single report
Philip Ewels et al.
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Yi Wang et al.
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The Listeria monocytogenes Core-Genome Sequence Typer (LmCGST): a bioinformatic pipeline for molecular characterization with next-generation sequence data
Arthur W. Pightling et al.
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Shannon M. Soucy et al.
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Trimmomatic: a flexible trimmer for Illumina sequence data
Anthony M. Bolger et al.
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Bruce J. Walker et al.
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Martin C. J. Maiden et al.
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