QIIME2 pipeline for ITS2-based nemabiome sequencing in veterinary species and the importance of analysis parameters.

ABSTRACT:

Background

Deep amplicon sequencing of nematode internal transcribed spacer 2 (ITS2), also referred to as the "nemabiome," has been increasingly used in veterinary hosts to study gastrointestinal nematodes. While post-sequencing bioinformatic pipelines such as DADA2 and mothur have been optimized, most researchers typically use the DADA2 pipeline in R. For optimal performance, DADA2 needs parameter tuning, which is hard for novices.

Methods

In this study, we present an implementation of the DADA2 pipeline within QIIME2 for nemabiome analysis and compare its performance against the commonly used R-based DADA2 pipeline. To evaluate performance against samples with known composition, we generated simulated nemabiome datasets representing canine, ruminant, and equine nematode co

SUBMITTER: Jesudoss Chelladurai JRJ 

PROVIDER: S-EPMC12822254 | biostudies-literature | 2025 Dec

REPOSITORIES: biostudies-literature