<commit_before>.. AMPtk documentation master file, created by
   sphinx-quickstart on Tue Sep 12 09:56:49 2017.
   You can adapt this file completely to your liking, but it should at least
   contain the root `toctree` directive.

AMPtk documentation
=================================

.. toctree::
   :hidden:
  
   overview
   quick-start
   file-formats
   pre-processing
   clustering
   filtering
   taxonomy
   commands
   downstream


AMPtk is a series of scripts to process NGS amplicon data using USEARCH and VSEARCH, it can also be used to process any NGS amplicon data and includes databases setup for analysis of fungal ITS, fungal LSU, bacterial 16S, and insect COI amplicons. It can handle Ion Torrent, MiSeq, and 454 data. At least USEARCH v9.1.13 and VSEARCH v2.2.0 are required as of AMPtk v0.7.0.


Citation
==================
.. code-block:: none

	<NAME>, <NAME>, <NAME>, <NAME>. 2018. Non-biological synthetic spike-in controls 
		and the AMPtk software pipeline improve mycobiome data. PeerJ 6:e4925; 
		DOI 10.7717/peerj.4925.	https://peerj.com/articles/4925/


Install
==================
There are several ways to install AMPtk, the easiest and recommended way is with Conda

.. code-block:: none
     
	#setup your conda env with bioconda, type the following in order to setup channels
	conda config --add channels defaults
	conda config --add channels conda-forge
	conda config --add channels bioconda
	
	#create amptk env (optional)
	conda create -n amptk amptk
	
	#UPDATE 2/9/2019: Conda solver seems to hang, if taking forever try this
	conda create -n amptk
	conda create -n amptk bioconductor-dada2 bioconductor-phyloseq biom-format \
	     biopython matplotlib natsort numpy pandas pigz psutil python-edlib r-base r-dt \
	     r-htmltools r-plotly seaborn vsearch
	conda activate amptk
	conda install amptk
	

You can install the python portion of AMPtk with pip, but you will need to then install the external dependencies such as usearch, vsearch, DADA2 and the amptk stats script will need to install R dependencies.

.. code-block:: none

	pip install amptk 
	
	
Users can also install manually, download a `release <https://github.com/nextgenusfs/amptk/releases>`_. You can also build the latest unreleased version from github:<commit_msg>change in conda install cmd<commit_after>.. AMPtk documentation master file, created by
   sphinx-quickstart on Tue Sep 12 09:56:49 2017.
   You can adapt this file completely to your liking, but it should at least
   contain the root `toctree` directive.

AMPtk documentation
=================================

.. toctree::
   :hidden:
  
   overview
   quick-start
   file-formats
   pre-processing
   clustering
   filtering
   taxonomy
   commands
   downstream


AMPtk is a series of scripts to process NGS amplicon data using USEARCH and VSEARCH, it can also be used to process any NGS amplicon data and includes databases setup for analysis of fungal ITS, fungal LSU, bacterial 16S, and insect COI amplicons. It can handle Ion Torrent, MiSeq, and 454 data. At least USEARCH v9.1.13 and VSEARCH v2.2.0 are required as of AMPtk v0.7.0.


Citation
==================
.. code-block:: none

	<NAME>, <NAME>, <NAME>, <NAME>. 2018. Non-biological synthetic spike-in controls 
		and the AMPtk software pipeline improve mycobiome data. PeerJ 6:e4925; 
		DOI 10.7717/peerj.4925.	https://peerj.com/articles/4925/


Install
==================
There are several ways to install AMPtk, the easiest and recommended way is with Conda

.. code-block:: none
     
	#setup your conda env with bioconda, type the following in order to setup channels
	conda config --add channels defaults
	conda config --add channels conda-forge
	conda config --add channels bioconda
	
	#create amptk env (optional)
	conda create -n amptk amptk
	
	#UPDATE 2/9/2019: Conda solver seems to hang, if taking forever try this
	conda create -n amptk
	conda install -n amptk bioconductor-dada2 bioconductor-phyloseq biom-format \
	     biopython matplotlib natsort numpy pandas pigz psutil python-edlib r-base r-dt \
	     r-htmltools r-plotly seaborn vsearch
	conda activate amptk
	conda install amptk
	

You can install the python portion of AMPtk with pip, but you will need to then install the external dependencies such as usearch, vsearch, DADA2 and the amptk stats script will need to install R dependencies.

.. code-block:: none

	pip install amptk 
	
	
Users can also install manually, download a `release <https://github.com/nextgenusfs/amptk/releases>`_. You can also build the latest unreleased version from github:
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