Read-SpaM

Read-SpaM performs alignment-free, assembly-free comparison of bacterial genomes from unassembled sequencing reads to estimate phylogenetic distances under low sequencing coverage.

Key Features:

• Alignment-Free and Assembly-Free: Compares genomic sequences directly from unassembled reads without requiring multiple sequence alignment or genome assembly.
• Low-Coverage Sequencing Compatibility: Operates on low-coverage sequencing reads to enable analysis when sequencing depth is limited.
• Phylogenetic Distance Estimation: Estimates phylogenetic distances between taxa, including cases with substantial evolutionary divergence and minimal data.

Scientific Applications:

• Phylogeny Reconstruction: Enables reconstruction of phylogenetic relationships without complete genome assemblies.
• Species Identification: Supports species identification from small sequencing samples for biodiversity and ecological studies.
• Bacterial Strain Typing: Facilitates bacterial strain typing for diagnostics, infection tracking, and outbreak analysis.

Methodology:

Adapts the Filtered Spaced-Word Matches (FSWM) approach to analyze unassembled sequencing reads and estimates phylogenetic distances; evaluated via simulated test runs on semi-artificial and real-world bacterial genomes.