Metadata-Version: 1.2
Name: q2-itsxpress
Version: 1.7.2
Summary: A QIIME2 plugin to trim ITS regions using ITSxpress
Home-page: https://github.com/usda-ars-gbru/q2_itsxpress
Author: Adam R. Rivers, Kyle C. Weber
Author-email: adam.rivers@ars.usda.gov, kweber1@ufl.edu
License: License :: CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
Description: Q2_ITSxpress: A Qiime2 plugin to rapidly trim the Internally transcribed spacer (ITS) region of FASTQ files
        ===========================================================================================================
        .. image:: https://travis-ci.org/USDA-ARS-GBRU/q2_itsxpress.svg?branch=master
          :target: https://travis-ci.org/USDA-ARS-GBRU/q2_itsxpress
        
        .. image:: https://codecov.io/gh/USDA-ARS-GBRU/q2_itsxpress/branch/master/graph/badge.svg
          :target: https://codecov.io/gh/USDA-ARS-GBRU/q2_itsxpress
        
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        .. image:: https://zenodo.org/badge/138209572.svg
           :target: https://zenodo.org/badge/latestdoi/138209572
        
        
        Authors
        -------
        * Adam R. Rivers, US Department of Agriculture, Agricultural Research Service
        * Kyle C. Weber, US Department of Agriculture, Agricultural Research Service
        
        Citation
        --------
        Rivers AR, Weber KC, Gardner TG et al. ITSxpress: Software to rapidly trim
        internally transcribed spacer sequences with quality scores for marker gene
        analysis. F1000Research 2018, 7:1418. doi: `10.12688/f1000research.15704.1`_
        
        .. _`10.12688/f1000research.15704.1`: https://doi.org/10.12688/f1000research.15704.1
        
        Introduction
        ------------
        
        The internally transcribed spacer (ITS) is a region between the small subunit
        and large subunit rRNA genes. In is a commonly used phylogenetic marker for
        Fungi and other Eukaryotes. The ITS contains the 5.8s gene and two variable
        length spacer regions. In amplicon sequencing studies it is common practice to
        trim off the conserved (SSU, 5,8S or LSU) regions. Bengtsson-Palme et al. (2013)
        published a software package ITSx_ to do this.
        
        Q2_ITSxpress extends this work by rapidly trimming FASTQ sequences within
        Qiime2.  Q2_ITSxpress is the Qiime2 plugin version of the stand alone command
        line utility ITSxpress_. Q2_ITSxpress is designed to support the calling of
        exact sequence variants rather than OTUs. This newer method of sequence
        error-correction requires quality score data from each sequence, so each input
        sequence must be trimmed. ITSxpress makes this possible by taking FASTQ data,
        de-replicating the sequences then identifying the start and stop sites using
        HMMSearch. Results are parsed and the trimmed files are returned. The ITS1,
        ITS2 or the entire ITS region including the 5.8s rRNA gene can be selected.
        ITSxpress uses the hmm models from ITSx so results are nearly identical.
        
        
        Requirements/Dependencies
        -------------------------
        
        * Qiime2 is required to run Q2-itsxpress (for stand alone software see ITSxpress_)
        * To install Qiime2 follow these instructions: https://docs.qiime2.org/2018.8/install/
        
        Q2_itsxpress Installation
        -------------------------
        
        1. Activate the Qiime2 conda environment
        
        .. code-block:: bash
        
          source activate qiime2-2018.8
        
        2. Install Q2_itsxpress using BioConda_. Be sure to install Q2_itsxpres in the Qiime2 environment.
        
        .. code-block:: bash
        
          conda install -c bioconda itsxpress
          pip install q2-itsxpress
        
        3. In your Qiime2 environment, refresh the plugins.
        
        .. code-block:: bash
        
          qiime dev refresh-cache
        
        4. Check to see if the ITSxpress plugin is installed. You should see an output similar to the image below.
        
        .. code-block:: bash
        
          qiime itsxpress
        
        .. image:: ../../screenshot.png
        
        Usage
        -----
        
        Within Qiime2 you can trim paired-end or single-end reads using these commands
        
        .. code-block:: bash
        
          qiime itsxpress trim-pair
        
          qiime itsxpress trim-pair-output-unmerged
        
          qiime itsxpress trim-single
        
        1. qiime itsxpress trim-single
        
          This command takes single-end data and returns trimmed reads. The sequence may
          have been merged previously or have been generated from a long read technology
          like PacBio. Merged and long reads trimmed by this function can be used by
          Deblur but only long reads (not merged reads) trimmed by this function should
          be passed to Dada2. Its statistical model for estimating error rates was not
          designed for pre-merged reads.
        
        +----------------------------------+---------------------------------------------------------------------------------------+
        |    Command-requirement           | Description                                                                           |
        +----------------------------------+---------------------------------------------------------------------------------------+
        |   --i-per-sample-sequences       | - The artifact that contains the sequence file(s).                                    |
        + 			           + - Either Joined Paired or just a single fastq.                                        +
        |                                  | - One file sequence in the qza data folder.                                           |
        +----------------------------------+---------------------------------------------------------------------------------------+
        |       --p-region                 | - The regions ITS2, ITS1, and ALL.                                                    |
        +----------------------------------+---------------------------------------------------------------------------------------+
        |				   | -	Select the taxonomic group sequenced: A, B, C, D, E, F, G, H, I, L, M, O, P,	   |
        +	--p-taxa		   +	Q, R, S, T, U, V, ALL.								   +
        | 				   |											   |
        +----------------------------------+---------------------------------------------------------------------------------------+
        |       --p-threads 	           | - The amount of threads to use.                                                       |
        +----------------------------------+---------------------------------------------------------------------------------------+
        |       --o-trimmed                | - The resulting trimmed sequences from ITSxpress in a qza format.                     |
        +----------------------------------+---------------------------------------------------------------------------------------+
        |      --cluster-id                | - The percent identity for clustering reads, set to 1 for exact dereplication.        |
        +----------------------------------+---------------------------------------------------------------------------------------+
        
        
        2. qiime itsxpress trim-pair
        
          This command takes paired-end data and returns merged, trimmed reads. The
          merged reads trimmed by this function can be used by Deblur but not
          Dada2. Its statistical model for estimating error rates was not
          designed for pre-merged reads, instead use `qiime itsxpress trim-pair-output-unmerged`.
        
        +----------------------------------+---------------------------------------------------------------------------------------+
        |    Command-requirement           | Description                                                                           |
        +----------------------------------+---------------------------------------------------------------------------------------+
        |   --i-per-sample-sequences       | - The artifact that contains the sequence file(s).                                    |
        + 			           + - Either Joined Paired or just a single fastq.                                        +
        |                                  | - One file sequence in the qza data folder.                                           |
        +----------------------------------+---------------------------------------------------------------------------------------+
        |       --p-region                 | - The regions ITS2, ITS1, and ALL.                                                    |
        +----------------------------------+---------------------------------------------------------------------------------------+
        |				   | -	Select the taxonomic group sequenced: A, B, C, D, E, F, G, H, I, L, M, O, P,	   |
        +	--p-taxa		   +	Q, R, S, T, U, V, ALL.								   +
        | 				   |											   |
        +----------------------------------+---------------------------------------------------------------------------------------+
        |       --p-threads 	           | - The amount of threads to use.                                                       |
        +----------------------------------+---------------------------------------------------------------------------------------+
        |       --o-trimmed                | - The resulting trimmed sequences from ITSxpress in a qza format.                     |
        +----------------------------------+---------------------------------------------------------------------------------------+
        |      --cluster-id                | - The percent identity for clustering reads, set to 1 for exact dereplication.        |
        +----------------------------------+---------------------------------------------------------------------------------------+
        
        3. qiime itsxpress trim-pair-output-unmerged
        
          This command takes paired-end data and returns unmerged, trimmed reads. The
          merged reads trimmed by this function can be used by Dada2 but not Deblur.
          For Deblur use `qiime itsxpress trim-pair`.
        
        +----------------------------------+---------------------------------------------------------------------------------------+
        |    Command-requirement           | Description                                                                           |
        +----------------------------------+---------------------------------------------------------------------------------------+
        |   --i-per-sample-sequences       | - The artifact that contains the sequence file.                                       |
        + 			           + - Only paired will work.                                                              +
        |                                  | - Two file sequences in the qza data folder.                                          |
        +----------------------------------+---------------------------------------------------------------------------------------+
        |       --p-region                 | - The regions ITS2, ITS1, and ALL.                                                    |
        +----------------------------------+---------------------------------------------------------------------------------------+
        |				   | -	Select the taxonomic group sequenced: A, B, C, D, E, F, G, H, I, L, M, O, P,	   |
        +	--p-taxa		   +	Q, R, S, T, U, V, ALL.								   +
        | 				   |											   |
        +----------------------------------+---------------------------------------------------------------------------------------+
        |       --p-threads 	           | - The amount of threads to use.                                                       |
        +----------------------------------+---------------------------------------------------------------------------------------+
        |       --o-trimmed                | - The resulting trimmed sequences from ITSxpress in a qza format.                     |
        +----------------------------------+---------------------------------------------------------------------------------------+
        |      --cluster-id                | - The percent identity for clustering reads, set to 1 for exact dereplication.        |
        +----------------------------------+---------------------------------------------------------------------------------------+
        
        Taxa Key
        --------
        
        +-+-------------------------------------+
        |A| Alveolata				|
        +-+-------------------------------------+
        |B| Bryophyta				|
        +-+-------------------------------------+
        |C| Bacillariophyta			|
        +-+-------------------------------------+
        |D| Amoebozoa				|
        +-+-------------------------------------+
        |E| Euglenozoa				|
        +-+-------------------------------------+
        |F| Fungi				|
        +-+-------------------------------------+
        |G| Chlorophyta (green algae)		|
        +-+-------------------------------------+
        |H| Rhodophyta (red algae)		|
        +-+-------------------------------------+
        |I| Phaeophyceae (brown algae)		|
        +-+-------------------------------------+
        |L| Marchantiophyta (liverworts)	|
        +-+-------------------------------------+
        |M| Metazoa				|
        +-+-------------------------------------+
        |O| Oomycota				|
        +-+-------------------------------------+
        |P| Haptophyceae (prymnesiophytes)	|
        +-+-------------------------------------+
        |Q| Raphidophyceae			|
        +-+-------------------------------------+
        |R| Rhizaria				|
        +-+-------------------------------------+
        |S| Synurophyceae			|
        +-+-------------------------------------+
        |T| Tracheophyta (higher plants)	|
        +-+-------------------------------------+
        |U| Eustigmatophyceae			|
        +-+-+-----------------------------------+
        |ALL| All				|
        +---+-----------------------------------+
        
        
        
        Example
        -------
        
        Use case: Trimming the ITS2 region from a fungal amplicon
        sequencing dataset with a PairedSequencesWithQuailty qza using two cpu threads.
        The example file used is in the Tests folder under paired.qza.
        
        .. code:: bash
        
          qiime itsxpress trim-pair --i-per-sample-sequences ~/parired.qza --p-region ITS2 \
          --p-taxa F --p-threads 2 --o-trimmed ~/Desktop/out.qza
        
        License information
        -------------------
        
        This software is a work of the United States Department of Agriculture,
        Agricultural Research Service and is released under a Creative Commons CC0
        public domain attribution.
        
        .. _ITSxpress: https://github.com/USDA-ARS-GBRU/itsxpress
        .. _ITSx: http://microbiology.se/software/itsx/
        .. _BioConda: https://bioconda.github.io/
        
Keywords: Amplicon sequencing fungal ITS QIIME2
Platform: UNKNOWN
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.5
Classifier: Development Status :: 3 - Alpha
Requires-Python: >3.5
