Amplicon_Sequencing_Worfklow download

This is a collection of scripts and instructions on how to analyzing amplicon sequence data (i.e., 16S, ITS2, & other marker genes). I created this workflow to create a consistent set of methods for analyzing amplicon sequence data, from when you first receive the sequence data to statistical analyses & data visualization. All you need is to have the latest version of R installed, some experience with the command line & shell, and enough memory to run all of the programs. There are also instructions provided in case you are running these analyses via a computing cluster/Slurm workload manager.

You can choose to go through the workflow using either an Rmd script, an html file, or a PDF, or via the homepage link provided.

If you have questions or concerns, please don't hesitate to reach out. Thanks!

Project Samples

Example Figure: Microbial Relative Abundance by Class

Example Figure: Microbial Taxonomic Summary

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License

MIT License

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Additional Project Details

Programming Language

R, Unix Shell

Related Categories

Unix Shell Molecular Science Software, Unix Shell Ecosystem Sciences Software, Unix Shell Bio-Informatics Software, R Molecular Science Software, R Ecosystem Sciences Software, R Bio-Informatics Software

Registered

2021-12-20

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