Package: itsxpress
AuthorAdam R. Rivers, US Department of Agriculture, Agricultural Research ServiceSveinn V. Einarsson, US Department of Agriculture, Agricultural Research ServiceCitationRivers AR, Weber KC, Gardner TG et al. ITSxpress: Software to rapidly trim
internally transcribed spacer sequences with quality scores for marker gene
analysis [version 1]. F1000Research 2018, 7:1418
(doi:10.12688/f1000research.15704.1)This is the end of life version 1 ITSxpress.
The new version 2 of ITSxpress, has the Qiime2 plugin built in with the command line version of ITSxpress. See
master branch of ITSxpress.IntroductionThe internally transcribed spacer region is a region between highly conserved the small
subunit (SSU) of rRNA and the large subunit (LSU) of the rRNA. In Eukaryotes it contains
the 5.8s genes 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 software the software packageITSxto do this.ITSxpress is designed to support the calling of exact sequence variants rather thanOTUs.
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 model from ITSx so results are comparable.ITSxpress is also available as aQIIME2 PluginInstallationThis is the installation of the final iteration of ITSxpress version 1: (BBmap is no longer used in ITSxpress version 2):This version should primarily be used for reproducability with other datasets, which used ITSxpress =<1.8.1The new version 2 is compatible with the newer versions of Qiime2If you want to install this iteration of ITSxpress with Qiime2, then you you need to follow the install instructions here:QIIME2 PluginSince this version is no longer supported, youmustcreate a new conda environment in order for the depenendencies to be compatible.Example on how to install and create new conda environment for this version of ITSxpress. We are using mamba because it resolves packages better and faster, but conda can be substituted.Information on installing mamba or micromamba (either highly recommended) can be found here:mamba installation guidemambacreate-nITSxpress_V1EOLpython=3.8.13mambaactivateITSxpress_V1EOL#orcondacreate-nITSxpress_V1EOLpython=3.8.13condaactivateITSxpress_V1EOLITSxpress can be installed in 3 ways:Bioconda:(preferred method because it handles dependencies):mambainstall-y-cbiocondaitsxpress==1.8.1Pip:https://pypi.org/project/itsxpress/:If using Pip, you will need to specify the versions of the dependencies listed below before installing itsxpressmambainstall-y-cbiocondahmmer==3.1b2mambainstall-y-cbiocondabbmap==38.69mambainstall-y-cbiocondavsearch==2.21.1pipinstallitsxpressThe Github repository:https://github.com/USDA-ARS-GBRU/itsxpressgitclone-branch1.8.1-EOLhttps://github.com/USDA-ARS-GBRU/itsxpress.gitDependenciesThis software requires Vsearch=2.21.1, BBtools=38.69, Hmmer=3.1b2 and Biopython>=1.79. Bioconda
takes care of this for you so it is the preferred installation method.UsageOptionDescription-h, –helpShow this help message and exit.–fastqA.fastq,.fq,.fastq.gzor.fq.gzfile.
Interleaved or not. Required.–single_endA flag to specify that the fastq file is single-ended (not
paired). Default is false.–fastq2A.fastq,.fq,.fastq.gzor.fq.gzfile
representing read 2 if present, optional.–outfileThe trimmed FASTQ file, if it ends ingzit will be
gzipped.–outfile2The trimmed FASTQ read 2 file, if it ends ingzit will
be gzipped. If used, reads will be retuned as unmerged pairs
rather than than merged.–tempdirSpecify the temp file directory. Default is None.–keeptempShould intermediate files be kept? Default is false.–regionOptions : {ITS2, ITS1, ALL}–taxaSelect the taxonomic group sequenced: {Alveolata, Bryophyta,
Bacillariophyta, Amoebozoa, Euglenozoa, Fungi, Chlorophyta,
Rhodophyta, Phaeophyceae, Marchantiophyta, Metazoa, Oomycota,
Haptophyceae, Raphidophyceae, Rhizaria, Synurophyceae,
Tracheophyta, Eustigmatophyceae, All}. Default Fungi.–cluster_idThe percent identity for clustering reads range [0.99-1.0],
set to 1 for exact de-replication. Default 1.0.–logLog file. Default is ITSxpress.log.–threadsNumber of processor threads to use. Default is 1.–reversed_primersPrimers are in reverse orientation as in Taylor et al. 2016,
DOI:10.1128/AEM.02576-16. If selected ITSxpress returns
trimmed reads flipped to the forward orientation–allow_staggered_readsAllow merging staggered reads with –fastq_allowmergestagger
for Vsearch –fastq_mergepairs. See Vsearch documentation.
(Optional) Default is true.ExamplesUse case 1: Trimming the ITS2 region from a fungal amplicon sequencing dataset with
forward and reverse gzipped FASTQ files using two cpu threads. Return a single merged file for use in Deblur.itsxpress--fastqr1.fastq.gz--fastq2r2.fastq.gz--regionITS2\--taxaFungi--loglogfile.txt--outfiletrimmed_reads.fastq.gz--threads2ITSxpress can take gzipped or un-gzipped FASTQ files and it can write gzipped or
un-gzipped FASTQ files. It expects FASTQ files to end in: .fq, .fastq, .fq.gz or fastq.gz.Use case 2: Trimming the ITS2 region from a fungal amplicon sequencing dataset with
forward and reverse gzipped FASTQ files using two cpu threads. Return a forward
and reverse read files  for use in Dada2.itsxpress--fastqr1.fastq.gz--fastq2r2.fastq.gz--regionITS2\--taxaFungi--loglogfile.txt--outfiletrimmed_reads.fastq.gz--threads2ITSxpress can take gzipped or un-gzipped FASTQ files and it can write gzipped or
un-gzipped FASTQ files. It expects FASTQ files to end in: .fq, .fastq, .fq.gz or fastq.gz.Use case 3: Trimming the ITS2 region from a fungal amplicon sequencing dataset with
an interleaved gzipped FASTQ files using two cpu threads. Return a single merged file for use in Deblur.itsxpress--fastqinterleaved.fastq.gz--regionITS2--taxaFungi\--loglogfile.txt--outfiletrimmed_reads.fastq.gz--threads2Use case 4: Trimming the ITS2 region from a fungal amplicon sequencing dataset with
an single-ended gzipped FASTQ files using two cpu threads.itsxpress--fastqsingle-end.fastq.gz--single_end--regionITS2--taxaFungi\--loglogfile.txt--outfiletrimmed_reads.fastq.gz--threads2Single ended data is less common and may come from a dataset where the reads have already
been merged.Use case 5: Trimming the ITS1 region from a Alveolata amplicon sequencing dataset with
an interleaved gzipped FASTQ files using 8 cpu threads.itsxpress--fastqinterleaved.fastq.gz--regionITS1--taxaAlveolata\--loglogfile.txt--outfiletrimmed_reads.fastq.gz--threads8License informationThis 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.