BioInformatic script for microbiome study
Include the following folders:
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BioBakery: Scripts for running the different biobakery tools from the Huttenhower Lab set of bioinformatic tools. See GitHub: https://github.com/biobakery/biobakery or webpage: https://huttenhower.sph.harvard.edu/tools/
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RScript: Templates for sequencing data processing and analysis. Scripts written on RStudio in a R Markdown format.
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mOTUs: Scripts for running mOTUs profiler. From the Sunagawa lab: https://motu-tool.org/ or see GitHub: https://github.com/motu-tool/mOTUs
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Preprocessing: Scripts for cleaning shotgun metagenomic sequencing data with FastP and remove host DNA sequences with Bowtie2.
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SRA: Scripts for downloading publicly available sequencing data from NCBI SRA run selector.
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RGI: Scripts for running the Resistance Gene Identifier (RGI) from CARD. See GitHub: https://github.com/arpcard/rgi