# AmpSeeker

Welcome to the [AmpSeeker](https://github.com/sanjaynagi/ampseeker/) documentation!

AmpSeeker is a computational pipeline to analyse Illumina amplicon sequencing data from any organism. The workflow applies a range of standard analyses for amplicon sequencing data, such as quality control, alignment, variant calling, interactive PCAs, sample maps, coverage and variant analyses. This website will help you install and configure the workflow to apply it to your own data.

Upon completion of the workflow, AmpSeeker builds a local webpage with interactive plots and tables to conveniently explore the results. The webpage is built using a combination of [papermill](https://github.com/nteract/papermill) and [Jupyter-book](https://jupyterbook.org/en/stable/intro.html).

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# User guide

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