ITSx

Introduction

“ITSx is an open source software utility to extract the highly variable ITS1 and ITS2 subregions from ITS sequences, which is commonly used as a molecular barcode for e.g. fungi.”

Available on Crunchomics: No

Installation

ITSx can be installed from scratch but below is the code needed to install the software with mamba.

If there is an issue with the mamba/conda installation, the software can also be downloaded with wget https://microbiology.se/sw/ITSx_1.1.3.tar.gz. After the download, decompress the folder and follow the information in the readme.txt. The download also comes with a test.fasta which can be used to test either installation.

Data for testing can also be found here.

mamba create -n fungi_its
mamba install -n fungi_its -c bioconda itsx

Usage

  • Required input: FASTA format (aligned or unaligned, DNA or RNA)

  • Generated output:

    • one summary file of the entire run
    • one more detailed table containing the positions in the respective sequences where the ITS subregions were found
    • one “semi-graphical” representation of hits
    • one FASTA file of all identified ITS sequences
    • one FASTA file for the ITS1 and ITS2 regions
    • if entries that did not contain any ITS region are found, a list of sequence IDs representing those entries (optional)

  • Useful arguments (not extensive, check manual for all arguments):

    • --save_regions: Get all regions of interest, not only ITS1/2
    • -E {value}: E-value cutoff (default 1e-5)
    • -S {value}: Domain score cutoff (default 0)
    • --cpu {value }: Number of cpus to use (default 1)
    • --multi_thread {T/F}: Multi-thread the HMMER-search. On (T) by default if the number of CPUs/cores is larger than one (–cpu option > 1), else off (F)
    • --preserve {T/F}: If on, ITSx will preserve the sequence headers from the input file instead of replacing them with ITSx headers in the output. Off (F) by default.
    • --only_full {T/F}: If true, the output is limited to full-length ITS1 and ITS2 regions only. Off (F) by default.
    • --minlen {value} Minimum length the ITS regions must be to be outputted in the concatenated file (see –concat above). Default is zero (0).

Example code

#activate the right environment
mamba activate fungi_its

#download data for testing the installation (optional)
mkdir testing
wget -P testing https://raw.githubusercontent.com/ScienceParkStudyGroup/software_information/main/data/itsx/test.fasta

#testrun (adjust path of test.fasta to where ever you downloaded the software)
ITSx -i testing/test.fasta --save_regions all -o testing/ITS_test_v1


#deactivate environment (if using environment)
mamba deactivate

Regions extracted from test file (notice how the full fasta ONLY contains sequences with all regions):

  • testing/ITS_test_v1.5_8S.fasta:50
  • testing/ITS_test_v1.ITS1.fasta:50
  • testing/ITS_test_v1.ITS2.fasta:50
  • testing/ITS_test_v1.LSU.fasta:32
  • testing/ITS_test_v1.SSU.fasta:31
  • testing/ITS_test_v1.full.fasta:19
  • testing/ITS_test_v1_no_detections.fasta:0
  • testing/test.fasta:50

References

Bengtsson-Palme, Johan, Martin Ryberg, Martin Hartmann, Sara Branco, Zheng Wang, Anna Godhe, Pierre De Wit, et al. 2013. “Improved Software Detection and Extraction of ITS1 and ITS2 from Ribosomal ITS Sequences of Fungi and Other Eukaryotes for Analysis of Environmental Sequencing Data.” Methods in Ecology and Evolution 4 (10): 914–19. https://doi.org/10.1111/2041-210X.12073.