SOAPMetaS

SOAPMetaS profiles large metagenomic datasets using marker genes and Apache Spark for distributed computation.

Key Features:

• Marker gene-based profiling: Utilizes marker genes to profile multiple samples simultaneously.
• High performance and scalability: Processes 80 FASTQ samples totaling 416 GiB in approximately half an hour on distributed clusters.
• Species-level accuracy: Achieves species profiling accuracy comparable to MetaPhlAn2.
• Distributed computing compatibility: Runs on local setups, Spark standalone clusters, and YARN clusters and is executed via spark-submit on Apache Spark.

Scientific Applications:

• Large-scale metagenomic profiling: Enables analysis of microbial community composition across large datasets.
• "meph" mode: Recommended for analysis of novel microbial communities using an approach aligned with MetaPhlAn2.
• "comg" mode: Suitable for samples from known microbial communities with a predefined gene set.

Methodology:

Implements marker gene-based profiling in Java and leverages Apache Spark for distributed execution, launched via spark-submit on local, Spark standalone, or YARN clusters.