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ARS Home » Southeast Area » Stoneville, Mississippi » Genomics and Bioinformatics Research » Research » Publications at this Location » Publication #419179
Research Project: Integrative Applied Agricultural Genomics and Bioinformatics Research

Location: Genomics and Bioinformatics Research

Title: ITSxpress Version 2: Software to rapidly trim internal transcribed spacer sequences with quality scores for amplicon sequencing

Author
item EINARSSON, SVEINN - University Of Florida
item Rivers, Adam

Submitted to: Microbiology Spectrum
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/19/2024
Publication Date: 11/5/2024
Citation: Einarsson, S.V., Rivers, A.R. 2024. ITSxpress Version 2: Software to rapidly trim internal transcribed spacer sequences with quality scores for amplicon sequencing. Microbiology Spectrum. https://doi.org/10.1128/spectrum.00601-24.
DOI: https://doi.org/10.1128/spectrum.00601-24

Interpretive Summary: The ribosomal RNA (rRNA) internal transcribed spacer (ITS) is a gene commonly used to identify fungi and other eukaryotic organisms when sequencing DNA from environmental samples. To identify and count ITS sequences the sequences need to be trimmed to the exact ITS region in the middle. The software ITSxpress does this trimming as a stand-alone program or a plug-in for the popular micrtbiome analysis program QIIME2. This paper explains the improvements made to ITSxpress in version 2. This version has has been refactored to simplify installation, reduce dependencies, return more trimmed reads and add support for more sequence types.

Technical Abstract: The nuclear ribosomal RNA (rRNA) internal transcribed spacer (ITS) regions are commonly used to identify fungi and other eukaryotic taxa in amplicon sequencing. The highly conserved rRNA regions flanking the ITS are often trimmed before being used for taxonomic assignment. The Python software package ITSxpress rapidly trims single-end or paired-end sequences in FASTQ format for use in amplicon sequence variant clustering methods like DADA2. This new major release of ITSxpress improves the paired-end merging method, simplifies installation of the QIIME 2 ITSxpress plugin, removes major dependencies, adds use cases, and is compatible with newer compression formats. This paper discusses the modifications to ITSxpress that improve the output and user experience, leading to a major version increase.