HOPS_MALT

HOPS_MALT automates screening and authentication of pathogenic ancient DNA from metagenomic high-throughput sequencing datasets using MALT and MaltExtract.

Key Features:

• Automated Screening Pipeline: Automates high-throughput screening of metagenomic data for target pathogenic DNA sequences.
• Species Identification and Authenticity Verification: Identifies species present and evaluates authenticity of detected ancient DNA sequences.
• Integration with MALT and MaltExtract: Integrates MALT (MAkER Lab Tools) outputs with MaltExtract for downstream analysis.
• Configurable Analysis Parameters: Uses configuration files to specify MALT and MaltExtract parameters and preserve reproducible settings.
• Logging and Slurm Command Tracking: Generates log files that record commands submitted to the Slurm job scheduler for monitoring and troubleshooting.

Scientific Applications:

• Archaeological Pathogen Screening: Detects and authenticates pathogenic DNA in archaeological and ancient samples.
• Reconstruction of Past Microbial Ecosystems: Identifies ancient bacterial commensals and pathogens to inform past microbiome compositions.
• Historical Disease and Environmental Inference: Provides data to study historical disease dynamics and environmental conditions relevant to human history and evolution.

Methodology:

Implemented in Java; integrates MALT and MaltExtract; processes high-throughput metagenomic sequencing data; uses configuration files to set analysis parameters; records and submits commands to Slurm; employs heuristic operations for pathogen screening.