# itsxpress 1.8.0


{{< admonition success "Installed" true >}}
This software should be available with no extra configuration.
{{< /admonition >}}

## itsxpress-1.8.0

The 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)](https://doi.org/10.1111/2041-210X.12073) 
published software the software package
[ITSx](http://microbiology.se/software/itsx/) to do this.

ITSxpress is designed to support the calling of exact sequence variants rather
than [OTUs](https://doi.org/10.1038/ismej.2017.119).  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 ITS 1, 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 a
[QIIME2 Plugin](https://github.com/USDA-ARS-GBRU/q2_itsxpress)

-------------------------------------------------------------------------------

## Location

```console
$ which itsxpress
/local/cluster/bin/itsxpress
```

## help message

```console
$ itsxpress --help
usage: itsxpress [-h] --fastq FASTQ [--single_end] [--fastq2 FASTQ2] --outfile
                 OUTFILE [--outfile2 OUTFILE2] [--tempdir TEMPDIR]
                 [--keeptemp] --region {ITS2,ITS1,ALL}
                 [--taxa {Alveolata,Bryophyta,Bacillariophyta,Amoebozoa,Euglenozoa,Fungi,Chlorophyta,Rhodophyta,Phaeophyceae,Marchantiophyta,Metazoa,Oomycota,Haptophyceae,Raphidophyceae, Rhizaria,Synurophyceae,Tracheophyta,Eustigmatophyceae,All}]
                 [--cluster_id CLUSTER_ID] [--reversed_primers] [--log LOG]
                 [--threads THREADS]

ITSxpress: A python module to rapidly trim ITS amplicon sequences from Fastq
files.

optional arguments:
  -h, --help            show this help message and exit
  --fastq FASTQ, -f FASTQ
                        A .fastq, .fq, .fastq.gz or .fq.gz file. Interleaved
                        or not.
  --single_end, -s      A flag to specify that the FASTQ file is single-ended
                        (not paired). Default is false.
  --fastq2 FASTQ2, -f2 FASTQ2
                        A .fastq, .fq, .fastq.gz or .fq.gz file. representing
                        read 2 (optional)
  --outfile OUTFILE, -o OUTFILE
                        the trimmed Fastq file, if it ends in 'gz' it will be
                        gzipped
  --outfile2 OUTFILE2, -o2 OUTFILE2
                        the trimmed read 2 Fastq file, if it ends in 'gz' it
                        will be gzipped. If provided, reads will be returned
                        unmerged.
  --tempdir TEMPDIR     The temp file directory
  --keeptemp            Should intermediate files be kept?
  --region {ITS2,ITS1,ALL}
  --taxa {Alveolata,Bryophyta,Bacillariophyta,Amoebozoa,Euglenozoa,Fungi,Chlorophyta,Rhodophyta,Phaeophyceae,Marchantiophyta,Metazoa,Oomycota,Haptophyceae,Raphidophyceae, Rhizaria,Synurophyceae,Tracheophyta,Eustigmatophyceae,All}
                        The taxonomic group sequenced.
  --cluster_id CLUSTER_ID
                        The percent identity for clustering reads range
                        [0.99-1.0], set to 1 for exact dereplication.
  --reversed_primers, -rp
                        Primers 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
  --log LOG             Log file
  --threads THREADS     Number of processor threads to use.
```

software ref: <https://github.com/USDA-ARS-GBRU/itsxpress>  
research ref: <https://doi.org/10.12688/f1000research.15704.1>