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        "author": "Adam R. Rivers, Kyle C. Weber",
        "author_email": "adam.rivers@ars.usda.gov, kweber1@ufl.edu",
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        "classifiers": [
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            "Programming Language :: Python :: 3.5",
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        "description": "Q2_ITSxpress: A Qiime2 plugin to rapidly trim the Internally transcribed spacer (ITS) region of FASTQ files\n===========================================================================================================\n.. image:: https://travis-ci.org/USDA-ARS-GBRU/q2_itsxpress.svg?branch=master\n  :target: https://travis-ci.org/USDA-ARS-GBRU/q2_itsxpress\n\n.. image:: https://codecov.io/gh/USDA-ARS-GBRU/q2_itsxpress/branch/master/graph/badge.svg\n  :target: https://codecov.io/gh/USDA-ARS-GBRU/q2_itsxpress\n\n.. image:: https://api.codacy.com/project/badge/Grade/4d00341b4abc4e04a77cf5ca6674cd3c\n  :target: https://www.codacy.com/app/USDA-ARS-GBRU/q2_itsxpress?utm_source=github.com&utm_medium=referral&utm_content=USDA-ARS-GBRU/q2_itsxpress&utm_campaign=Badge_Grade\n\n.. image:: https://zenodo.org/badge/138209572.svg\n   :target: https://zenodo.org/badge/latestdoi/138209572\n\n\nAuthors\n-------\n* Adam R. Rivers, US Department of Agriculture, Agricultural Research Service\n* Kyle C. Weber, US Department of Agriculture, Agricultural Research Service\n\nCitation\n--------\nRivers AR, Weber KC, Gardner TG et al. ITSxpress: Software to rapidly trim\ninternally transcribed spacer sequences with quality scores for marker gene\nanalysis. F1000Research 2018, 7:1418. doi: `10.12688/f1000research.15704.1`_\n\n.. _`10.12688/f1000research.15704.1`: https://doi.org/10.12688/f1000research.15704.1\n\nIntroduction\n------------\n\nThe internally transcribed spacer (ITS) is a region between the small subunit\nand large subunit rRNA genes. In is a commonly used phylogenetic marker for\nFungi and other Eukaryotes. The ITS contains the 5.8s gene and two variable\nlength spacer regions. In amplicon sequencing studies it is common practice to\ntrim off the conserved (SSU, 5,8S or LSU) regions. Bengtsson-Palme et al. (2013)\npublished a software package ITSx_ to do this.\n\nQ2_ITSxpress extends this work by rapidly trimming FASTQ sequences within\nQiime2.  Q2_ITSxpress is the Qiime2 plugin version of the stand alone command\nline utility ITSxpress_. Q2_ITSxpress is designed to support the calling of\nexact sequence variants rather than OTUs. This newer method of sequence\nerror-correction requires quality score data from each sequence, so each input\nsequence must be trimmed. ITSxpress makes this possible by taking FASTQ data,\nde-replicating the sequences then identifying the start and stop sites using\nHMMSearch. Results are parsed and the trimmed files are returned. The ITS1,\nITS2 or the entire ITS region including the 5.8s rRNA gene can be selected.\nITSxpress uses the hmm models from ITSx so results are nearly identical.\n\n\nRequirements/Dependencies\n-------------------------\n\n* Qiime2 is required to run Q2-itsxpress (for stand alone software see ITSxpress_)\n* To install Qiime2 follow these instructions: https://docs.qiime2.org/2018.8/install/\n\nQ2_itsxpress Installation\n-------------------------\n\n1. Activate the Qiime2 conda environment\n\n.. code-block:: bash\n\n  source activate qiime2-2018.8\n\n2. Install Q2_itsxpress using BioConda_. Be sure to install Q2_itsxpres in the Qiime2 environment.\n\n.. code-block:: bash\n\n  conda install -c bioconda itsxpress\n  pip install q2-itsxpress\n\n3. In your Qiime2 environment, refresh the plugins.\n\n.. code-block:: bash\n\n  qiime dev refresh-cache\n\n4. Check to see if the ITSxpress plugin is installed. You should see an output similar to the image below.\n\n.. code-block:: bash\n\n  qiime itsxpress\n\n.. image:: ../../screenshot.png\n\nUsage\n-----\n\nWithin Qiime2 you can trim paired-end or single-end reads using these commands\n\n.. code-block:: bash\n\n  qiime itsxpress trim-pair\n\n  qiime itsxpress trim-pair-output-unmerged\n\n  qiime itsxpress trim-single\n\n1. qiime itsxpress trim-single\n\n  This command takes single-end data and returns trimmed reads. The sequence may\n  have been merged previously or have been generated from a long read technology\n  like PacBio. Merged and long reads trimmed by this function can be used by\n  Deblur but only long reads (not merged reads) trimmed by this function should\n  be passed to Dada2. Its statistical model for estimating error rates was not\n  designed for pre-merged reads.\n\n+----------------------------------+---------------------------------------------------------------------------------------+\n|    Command-requirement           | Description                                                                           |\n+----------------------------------+---------------------------------------------------------------------------------------+\n|   --i-per-sample-sequences       | - The artifact that contains the sequence file(s).                                    |\n+ \t\t\t           + - Either Joined Paired or just a single fastq.                                        +\n|                                  | - One file sequence in the qza data folder.                                           |\n+----------------------------------+---------------------------------------------------------------------------------------+\n|       --p-region                 | - The regions ITS2, ITS1, and ALL.                                                    |\n+----------------------------------+---------------------------------------------------------------------------------------+\n|\t\t\t\t   | -\tSelect the taxonomic group sequenced: A, B, C, D, E, F, G, H, I, L, M, O, P,\t   |\n+\t--p-taxa\t\t   +\tQ, R, S, T, U, V, ALL.\t\t\t\t\t\t\t\t   +\n| \t\t\t\t   |\t\t\t\t\t\t\t\t\t\t\t   |\n+----------------------------------+---------------------------------------------------------------------------------------+\n|       --p-threads \t           | - The amount of threads to use.                                                       |\n+----------------------------------+---------------------------------------------------------------------------------------+\n|       --o-trimmed                | - The resulting trimmed sequences from ITSxpress in a qza format.                     |\n+----------------------------------+---------------------------------------------------------------------------------------+\n|      --cluster-id                | - The percent identity for clustering reads, set to 1 for exact dereplication.        |\n+----------------------------------+---------------------------------------------------------------------------------------+\n\n\n2. qiime itsxpress trim-pair\n\n  This command takes paired-end data and returns merged, trimmed reads. The\n  merged reads trimmed by this function can be used by Deblur but not\n  Dada2. Its statistical model for estimating error rates was not\n  designed for pre-merged reads, instead use `qiime itsxpress trim-pair-output-unmerged`.\n\n+----------------------------------+---------------------------------------------------------------------------------------+\n|    Command-requirement           | Description                                                                           |\n+----------------------------------+---------------------------------------------------------------------------------------+\n|   --i-per-sample-sequences       | - The artifact that contains the sequence file(s).                                    |\n+ \t\t\t           + - Either Joined Paired or just a single fastq.                                        +\n|                                  | - One file sequence in the qza data folder.                                           |\n+----------------------------------+---------------------------------------------------------------------------------------+\n|       --p-region                 | - The regions ITS2, ITS1, and ALL.                                                    |\n+----------------------------------+---------------------------------------------------------------------------------------+\n|\t\t\t\t   | -\tSelect the taxonomic group sequenced: A, B, C, D, E, F, G, H, I, L, M, O, P,\t   |\n+\t--p-taxa\t\t   +\tQ, R, S, T, U, V, ALL.\t\t\t\t\t\t\t\t   +\n| \t\t\t\t   |\t\t\t\t\t\t\t\t\t\t\t   |\n+----------------------------------+---------------------------------------------------------------------------------------+\n|       --p-threads \t           | - The amount of threads to use.                                                       |\n+----------------------------------+---------------------------------------------------------------------------------------+\n|       --o-trimmed                | - The resulting trimmed sequences from ITSxpress in a qza format.                     |\n+----------------------------------+---------------------------------------------------------------------------------------+\n|      --cluster-id                | - The percent identity for clustering reads, set to 1 for exact dereplication.        |\n+----------------------------------+---------------------------------------------------------------------------------------+\n\n3. qiime itsxpress trim-pair-output-unmerged\n\n  This command takes paired-end data and returns unmerged, trimmed reads. The\n  merged reads trimmed by this function can be used by Dada2 but not Deblur.\n  For Deblur use `qiime itsxpress trim-pair`.\n\n+----------------------------------+---------------------------------------------------------------------------------------+\n|    Command-requirement           | Description                                                                           |\n+----------------------------------+---------------------------------------------------------------------------------------+\n|   --i-per-sample-sequences       | - The artifact that contains the sequence file.                                       |\n+ \t\t\t           + - Only paired will work.                                                              +\n|                                  | - Two file sequences in the qza data folder.                                          |\n+----------------------------------+---------------------------------------------------------------------------------------+\n|       --p-region                 | - The regions ITS2, ITS1, and ALL.                                                    |\n+----------------------------------+---------------------------------------------------------------------------------------+\n|\t\t\t\t   | -\tSelect the taxonomic group sequenced: A, B, C, D, E, F, G, H, I, L, M, O, P,\t   |\n+\t--p-taxa\t\t   +\tQ, R, S, T, U, V, ALL.\t\t\t\t\t\t\t\t   +\n| \t\t\t\t   |\t\t\t\t\t\t\t\t\t\t\t   |\n+----------------------------------+---------------------------------------------------------------------------------------+\n|       --p-threads \t           | - The amount of threads to use.                                                       |\n+----------------------------------+---------------------------------------------------------------------------------------+\n|       --o-trimmed                | - The resulting trimmed sequences from ITSxpress in a qza format.                     |\n+----------------------------------+---------------------------------------------------------------------------------------+\n|      --cluster-id                | - The percent identity for clustering reads, set to 1 for exact dereplication.        |\n+----------------------------------+---------------------------------------------------------------------------------------+\n\nTaxa Key\n--------\n\n+-+-------------------------------------+\n|A| Alveolata\t\t\t\t|\n+-+-------------------------------------+\n|B| Bryophyta\t\t\t\t|\n+-+-------------------------------------+\n|C| Bacillariophyta\t\t\t|\n+-+-------------------------------------+\n|D| Amoebozoa\t\t\t\t|\n+-+-------------------------------------+\n|E| Euglenozoa\t\t\t\t|\n+-+-------------------------------------+\n|F| Fungi\t\t\t\t|\n+-+-------------------------------------+\n|G| Chlorophyta (green algae)\t\t|\n+-+-------------------------------------+\n|H| Rhodophyta (red algae)\t\t|\n+-+-------------------------------------+\n|I| Phaeophyceae (brown algae)\t\t|\n+-+-------------------------------------+\n|L| Marchantiophyta (liverworts)\t|\n+-+-------------------------------------+\n|M| Metazoa\t\t\t\t|\n+-+-------------------------------------+\n|O| Oomycota\t\t\t\t|\n+-+-------------------------------------+\n|P| Haptophyceae (prymnesiophytes)\t|\n+-+-------------------------------------+\n|Q| Raphidophyceae\t\t\t|\n+-+-------------------------------------+\n|R| Rhizaria\t\t\t\t|\n+-+-------------------------------------+\n|S| Synurophyceae\t\t\t|\n+-+-------------------------------------+\n|T| Tracheophyta (higher plants)\t|\n+-+-------------------------------------+\n|U| Eustigmatophyceae\t\t\t|\n+-+-+-----------------------------------+\n|ALL| All\t\t\t\t|\n+---+-----------------------------------+\n\n\n\nExample\n-------\n\nUse case: Trimming the ITS2 region from a fungal amplicon\nsequencing dataset with a PairedSequencesWithQuailty qza using two cpu threads.\nThe example file used is in the Tests folder under paired.qza.\n\n.. code:: bash\n\n  qiime itsxpress trim-pair --i-per-sample-sequences ~/parired.qza --p-region ITS2 \\\n  --p-taxa F --p-threads 2 --o-trimmed ~/Desktop/out.qza\n\nLicense information\n-------------------\n\nThis software is a work of the United States Department of Agriculture,\nAgricultural Research Service and is released under a Creative Commons CC0\npublic domain attribution.\n\n.. _ITSxpress: https://github.com/USDA-ARS-GBRU/itsxpress\n.. _ITSx: http://microbiology.se/software/itsx/\n.. _BioConda: https://bioconda.github.io/\n\n\n",
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