ReporType

ReporType screens and types targeted loci of infectious agents by integrating quality control, assembly, and locus screening into a unified pipeline for pathogen genotyping.

Key Features:

• Multi-format input support: The pipeline accepts Illumina or Oxford Nanopore Technology (ONT) reads in FASTQ format, Sanger sequencing files in AB1 format, or FASTA files.
• Integrated software pipeline: ReporType combines multiple software tools for read quality control and de novo assembly, then applies ABRicate for locus screening.
• Pre-configured and custom databases: The tool is released with pre-prepared databases for some viruses and bacteria, and remains configurable to handle custom databases.
• Workflow management: The pipeline is developed using the snakemake workflow manager.
• Interpretable reporting: The pipeline produces easily interpretable reports for the identification of pathogen genotypes and screening of specific genomic loci.

Scientific Applications:

• Viral pathogen typing: ReporType has been validated for genotyping measles, Newcastle disease virus (NDV), Dengue virus (DENV), influenza, hepatitis C virus (HCV), and Human T-Cell Lymphotropic virus type 1 (HTLV-1).
• Bacterial pathogen typing: ReporType has been validated for characterizing Chlamydia trachomatis and Legionella pneumophila.
• Targeted locus screening: The pipeline enables screening of specific genomic loci across diverse pathogenic species.
• Pathogen genomics and epidemiology: ReporType supports infectious disease epidemiology and one health bioinformatics through rapid pathogen characterization and classification.

Methodology:

ReporType uses the snakemake workflow manager to integrate multiple software for read quality control and de novo assembly, then applies ABRicate for locus screening.