Package: q2-itsxpress
This is the end of life version 1 of q2_itsxpress and the command line version of ITSxpress. See
1.8.1-EOL branch of ITSxpress. The new version 2 of ITSxpress, has the Qiime2 plugin built in with command line version of ITSxpress.See ITSxpress 1.8.1-EOL branch here:ITSxpress-1.8.1-EOLAuthorsAdam R. Rivers, US Department of Agriculture, Agricultural Research ServiceKyle C. Weber, 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. F1000Research 2018, 7:1418. doi:10.12688/f1000research.15704.1IntroductionThe 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 packageITSxto 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 utilityITSxpress. 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/DependenciesQiime2 is required to run Q2-itsxpress (for stand alone software seeITSxpress)To install Qiime2 follow these instructions:https://docs.qiime2.org/2022.8/install/This end of life version 1 of q2-itsxpress and ITSxpress isONLYcompatible with Qiime2 version 2022.8. So make sure to follow the link above.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 guideQ2-itsxpress plugin installationExample on how to install and create new Qiime2-2022.8 environment.wgethttps://data.qiime2.org/distro/core/qiime2-2022.8-py38-osx-conda.ymlmambaenvcreate-nqiime2-2022.8--fileqiime2-2022.8-py38-osx-conda.ymlActivate the Qiime2 conda environmentmambaactivateqiime2-2022.8Install Q2_itsxpress usingBioConda. Be sure to install itsxpress and q2_itsxpress in the Qiime2 environment using the following commands.mambainstall-cbiocondaitsxpress==1.8.1pipinstallq2-itsxpressIn your Qiime2 environment, refresh the plugins.qiimedevrefresh-cacheCheck to see if the ITSxpress plugin is installed. You should see an output similar to the image below.qiimeitsxpressUsageWithin Qiime2 you can trim paired-end or single-end reads using these commandsqiimeitsxpresstrim-pairqiimeitsxpresstrim-pair-output-unmergedqiimeitsxpresstrim-singleqiime itsxpress trim-singleThis 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-requirementDescription–i-per-sample-sequencesThe artifact that contains the sequence file(s).Either Joined Paired or just a single fastq.One file sequence in the qza data folder.–p-regionThe regions ITS2, ITS1, and ALL.–p-taxaSelect the taxonomic group sequenced: A, B, C, D, E, F, G, H, I, L, M, O, P,
Q, R, S, T, U, V, ALL.–p-threadsThe amount of threads to use.–o-trimmedThe resulting trimmed sequences from ITSxpress in a qza format.–cluster-idThe percent identity for clustering reads, set to 1 for exact dereplication.qiime itsxpress trim-pairThis 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 useqiime itsxpress trim-pair-output-unmerged.Command-requirementDescription–i-per-sample-sequencesThe artifact that contains the sequence file(s).Either Joined Paired or just a single fastq.One file sequence in the qza data folder.–p-regionThe regions ITS2, ITS1, and ALL.–p-taxaSelect the taxonomic group sequenced: A, B, C, D, E, F, G, H, I, L, M, O, P,
Q, R, S, T, U, V, ALL.–p-threadsThe amount of threads to use.–o-trimmedThe resulting trimmed sequences from ITSxpress in a qza format.–cluster-idThe percent identity for clustering reads, set to 1 for exact dereplication.qiime itsxpress trim-pair-output-unmergedThis 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 useqiime itsxpress trim-pair.Command-requirementDescription–i-per-sample-sequencesThe artifact that contains the sequence file.Only paired will work.Two file sequences in the qza data folder.–p-regionThe regions ITS2, ITS1, and ALL.–p-taxaSelect the taxonomic group sequenced: A, B, C, D, E, F, G, H, I, L, M, O, P,
Q, R, S, T, U, V, ALL.–p-threadsThe amount of threads to use.–o-trimmedThe resulting trimmed sequences from ITSxpress in a qza format.–cluster-idThe percent identity for clustering reads, set to 1 for exact dereplication.Taxa KeyAAlveolataBBryophytaCBacillariophytaDAmoebozoaEEuglenozoaFFungiGChlorophyta (green algae)HRhodophyta (red algae)IPhaeophyceae (brown algae)LMarchantiophyta (liverworts)MMetazoaOOomycotaPHaptophyceae (prymnesiophytes)QRaphidophyceaeRRhizariaSSynurophyceaeTTracheophyta (higher plants)UEustigmatophyceaeALLAllExampleUse 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.qiimeitsxpresstrim-pair--i-per-sample-sequences~/parired.qza--p-regionITS2\--p-taxaF--p-threads2--o-trimmed~/Desktop/out.qzaLicense 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.