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        "description": "ITSxpress: Software to rapidly trim  the Internally transcribed spacer (ITS) region of FASTQ files\n==================================================================================================\n.. image:: https://travis-ci.org/USDA-ARS-GBRU/itsxpress.svg?branch=master\n    :target: https://travis-ci.org/USDA-ARS-GBRU/itsxpress\n\n.. image:: https://readthedocs.org/projects/itsxpress/badge/?version=latest\n    :target: https://itsxpress.readthedocs.io/en/latest/?badge=latest\n    :alt: Documentation Status\n\n.. image:: https://codecov.io/gh/USDA-ARS-GBRU/itsxpress/branch/master/graph/badge.svg\n  :target: https://codecov.io/gh/USDA-ARS-GBRU/itsxpress\n\n.. image:: https://api.codacy.com/project/badge/Grade/7e2a4c97cde74bccb3e84b706d7a2aa5\n  :target: https://www.codacy.com/app/GBRU/itsxpress?utm_source=github.com&utm_medium=referral&utm_content=USDA-ARS-GBRU/itsxpress&utm_campaign=Badge_Grade\n\n.. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.1304349.svg\n  :target: https://doi.org/10.5281/zenodo.1304349\n\nAuthor\n-------\n* Adam R. Rivers, US Department of Agriculture, Agricultural Research Service\n\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 [version 1; referees: awaiting peer review]. F1000Research 2018, 7:1418\n(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 region is a region between highly conserved the small\nsubunit (SSU) of rRNA and the large subunit (LSU) of the rRNA. In Eukaryotes it contains\nthe 5.8s genes and two variable length spacer regions. In amplicon sequencing studies it is\ncommon practice to trim off the conserved (SSU, 5,8S or LSU) regions. `Bengtsson-Palme\net al. (2013)`_ published software the software package ITSx_ to do this.\n\nITSxpress is designed to support the calling of exact sequence variants rather than OTUs_.\nThis newer method of sequence error-correction requires quality score data from each\nsequence, so each input sequence must be trimmed. ITSXpress makes this possible by\ntaking FASTQ data, de-replicating the sequences then identifying the start and stop\nsites using HMMSearch.  Results are parsed and the trimmed files are returned. The ITS 1,\nITS2 or the entire ITS region including the 5.8s rRNA gene can be selected. ITSxpress\nuses the hmm model from ITSx so results are comparable.\n\nITSxpress is also available as a `QIIME2 Plugin`_\n\n.. _`Bengtsson-Palme et al. (2013)`: https://doi.org/10.1111/2041-210X.12073\n.. _ITSx: http://microbiology.se/software/itsx/\n.. _OTUs: https://doi.org/10.1038/ismej.2017.119\n.. _`QIIME2 Plugin`: https://github.com/USDA-ARS-GBRU/q2_itsxpress\n\n\nInstallation\n-------------\nITSxpress can be installed from:\n\n1. Bioconda: (preferred method because it handles dependencies):\n\n.. code-block:: bash\n\n    conda install itsxpress\n\n2. Pip: https://pypi.org/project/itsxpress/:\n\n.. code-block:: bash\n\n    pip install itsxpress\n\n\n3. The Github repository: https://github.com/USDA-ARS-GBRU/itsxpress\n\n.. code-block:: bash\n\n    git clone https://github.com/USDA-ARS-GBRU/itsxpress.git\n\n\nDependencies\n-------------\nThe software requires Vsearch, BBtools, Hmmer >= 3.1b and Biopython. Bioconda\ntakes care of this for you so it is the preferred installation method.\n\n\nUsage\n---------\n\n-h, --help            \tShow this help message and exit.\n\n--fastq \t\t\t\tA ``.fastq``, ``.fq``, ``.fastq.gz`` or ``.fq.gz`` file. Interleaved\n                        \tor not. Required.\n\n--single_end \t\t\tA flag to specify that the fastq file is single-ended (not paired).\n                        \tsingle-ended (not paired). Default is false.\n\n--fastq2 \t\t\t\tA ``.fastq``, ``.fq``, ``.fastq.gz`` or ``.fq.gz`` file representing read 2 if present, optional.\n\n--outfile\t\t\t\tThe trimmed FASTQ file, if it ends in ``gz`` it will be gzipped.\n\n--outfile2\t\t\tThe trimmed FASTQ read 2 file, if it ends in ``gz`` it will be gzipped. If used, reads will be retuned as unmerged pairs rather than than merged.\n\n--tempdir\t\t\t\tSpecify the temp file directory. Default is None.\n\n--keeptemp\t\t\t\tShould intermediate files be kept? Default is false.\n\n--region \t\t\t\tOptions : {ITS2, ITS1, ALL}\n\n--taxa\t\t\t\t\tSelect the taxonomic group sequenced: {Alveolata, Bryophyta,\n\t\t\t\t\t\tBacillariophyta, Amoebozoa, Euglenozoa, Fungi, Chlorophyta,\n\t\t\t\t\t\tRhodophyta, Phaeophyceae, Marchantiophyta, Metazoa,\n\t\t\t\t\t\tOomycota, Haptophyceae, Raphidophyceae, Rhizaria, Synurophyceae,\n\t\t\t\t\t\tTracheophyta, Eustigmatophyceae, All}. Default Fungi.\n\n--cluster_id            The percent identity for clustering reads range [0.98-1.0], set to 1\n                        for exact dereplication. Default 0.995.\n\n--log\t\t          \tLog file. Default is ITSxpress.log.\n\n--threads\t\t     \tNumber of processor threads to use. Default is 1.\n\n\nExamples\n---------\n\nUse case 1: Trimming the ITS2 region from a fungal amplicon sequencing dataset with\nforward and reverse gzipped FASTQ files using two cpu threads. Return a single merged file for use in Deblur.\n\n.. code-block:: bash\n\n    itsxpress --fastq r1.fastq.gz --fastq2 r2.fastq.gz --region ITS2 \\\n    --taxa Fungi --log logfile.txt --outfile trimmed_reads.fastq.gz --threads 2\n\nITSxpress can take gzipped or un-gzipped FASTQ files and it can write gzipped or\nun-gzipped FASTQ files. It expects FASTQ files to end in: .fq, .fastq, .fq.gz or fastq.gz.\n\nUse case 2: Trimming the ITS2 region from a fungal amplicon sequencing dataset with\nforward and reverse gzipped FASTQ files using two cpu threads. Return a forward\nand reverse read files  for use in Dada2.\n\n.. code-block:: bash\n\n    itsxpress --fastq r1.fastq.gz --fastq2 r2.fastq.gz --region ITS2 \\\n    --taxa Fungi --log logfile.txt --outfile trimmed_reads.fastq.gz --threads 2\n\nITSxpress can take gzipped or un-gzipped FASTQ files and it can write gzipped or\nun-gzipped FASTQ files. It expects FASTQ files to end in: .fq, .fastq, .fq.gz or fastq.gz.\n\n\nUse case 3: Trimming the ITS2 region from a fungal amplicon sequencing dataset with\nan interleaved gzipped FASTQ files using two cpu threads. Return a single merged file for use in Deblur.\n\n.. code-block:: bash\n\n    itsxpress --fastq interleaved.fastq.gz  --region ITS2 --taxa Fungi \\\n    --log logfile.txt --outfile trimmed_reads.fastq.gz --threads 2\n\n\nUse case 4: Trimming the ITS2 region from a fungal amplicon sequencing dataset with\nan single-ended gzipped FASTQ files using two cpu threads.\n\n.. code-block:: bash\n\n    itsxpress --fastq single-end.fastq.gz --single_end --region ITS2 --taxa Fungi \\\n    --log logfile.txt --outfile trimmed_reads.fastq.gz --threads 2\n\nSingle ended data is less common and may come from a dataset where the reads have already\nbeen merged.\n\nUse case 5: Trimming the ITS1 region from a Alveolata amplicon sequencing dataset with\nan interleaved gzipped FASTQ files using 40 cpu threads.\n\n.. code-block:: bash\n\n    itsxpress --fastq interleaved.fastq.gz --region ITS1 --taxa Alveolata \\\n    --log logfile.txt --outfile trimmed_reads.fastq.gz --threads 40\n\n\nLicense information\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\n",
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