phyloFlash

phyloFlash reconstructs and analyzes small-subunit ribosomal RNA (SSU rRNA) genes from Illumina metagenomic and metatranscriptomic datasets to enable taxonomic profiling and linkage of SSU rRNA sequences to metagenome-assembled genomes (MAGs).

Key Features:

• Rapid Taxonomic Classification: Leverages a curated SSU rRNA reference database for rapid taxonomic classification of microbial taxa in Illumina metagenomic or metatranscriptomic datasets.
• Targeted Assembly: Employs targeted assembly using SPAdes to produce high-quality SSU rRNA assemblies with reduced chimerism compared to other reference-based assemblers.
• Graph-Based Linking: Integrates graph-based binning methods to link assembled SSU rRNAs with MAGs and support multisample comparisons.
• Efficient Data Processing: Uses BBmap for read mapping, achieving approximately fivefold faster processing than SortMeRNA while maintaining high sensitivity and selectivity on simulated metagenomes.

Scientific Applications:

• Domain-agnostic SSU rRNA profiling: Enables tracking and taxonomic profiling of organisms across eukaryotes, archaea, and bacteria using SSU rRNA genes.
• Recovery of taxa missing from MAGs: Facilitates detection and linkage of SSU rRNA genes that are often absent from metagenome-assembled genomes.
• Microbial diversity comparisons: Supports taxonomic profiling, targeted SSU rRNA assembly, and multisample visualization of microbial diversity within metagenomic workflows.

Methodology:

Uses BBmap for read mapping to a curated SSU rRNA reference database; performs targeted assembly with SPAdes (noting reduced chimerism versus other reference-based assemblers); applies graph-based binning to link assembled SSU rRNAs with MAGs; mapping performance reported relative to SortMeRNA on simulated metagenomes.