read2tree

read2tree infers phylogenetic trees directly from raw sequencing reads to enable large-scale phylogenomic and comparative genomic analyses without assembly or annotation.

Key Features:

• Direct raw-read processing: Processes raw sequencing reads into groups of corresponding genes by leveraging the OMA database for gene grouping.
• Pipeline bypass: Bypasses read filtering, genome assembly, gene prediction, annotation, all‑versus‑all sequence comparisons, orthology prediction, alignment, and concatenation.
• Benchmark speed: Demonstrates 10- to 100-fold faster runtimes than traditional assembly-based methods in benchmark tests.
• Accuracy and limitations: Achieves comparable or superior phylogenetic accuracy to assembly-based approaches, with reduced performance for very distant reference species or exceptionally high sequencing coverage.
• Empirical demonstrations: Reconstructed a yeast tree of life containing 435 species spanning ~590 million years and classified over 10,000 Coronaviridae samples, resolving diverse animal-derived sequences and near-identical SARS-CoV-2 genomes on a single tree.

Scientific Applications:

• Large-scale comparative genomics: Enables phylogenetic inference across extensive species sets directly from raw reads for broad comparative analyses.
• Evolutionary studies: Facilitates reconstruction of deep and shallow phylogenetic relationships for evolutionary investigations.
• Microbial taxonomy: Supports taxonomic classification of microbes through direct phylogenetic placement from sequencing reads.
• Virology research: Enables rapid phylogenetic classification and surveillance in virology, including analyses of Coronaviridae and SARS-CoV-2 samples.

Methodology:

Processes raw sequencing reads into gene groups using the OMA database and infers phylogenetic trees while omitting assembly, gene prediction, annotation, all‑versus‑all comparisons, orthology prediction, alignment, and concatenation.