CLAW

CLAW assembles chloroplast genomes from long-read (third-generation) sequencing data to enable reconstruction and comparative analysis for evolutionary, taxonomic, and agricultural research.

Key Features:

• Long-read assembly: Assembles chloroplast genomes using long-read (third-generation) sequencing data.
• Whole-library extraction: Leverages incidental chloroplast-derived reads present in whole-tissue or whole-genome long-read libraries originally generated for nuclear genome sequencing.
• Workflow engine: Implemented as a Snakemake workflow management system.
• Empirical validation: Validated using 19 publicly available reference chloroplast genome assemblies with corresponding long-read libraries from algae, monocots, and eudicots, producing assemblies with high fidelity to references.

Scientific Applications:

• Chloroplast genome reconstruction: Reconstruction of complete chloroplast genomes from long-read sequencing datasets.
• Phylogenomics and evolutionary analysis: Comparative and evolutionary analyses using assembled chloroplast genomes.
• Taxonomic identification: Species identification and barcoding based on chloroplast genome sequences.
• Crop improvement and agricultural biotechnology: Use of chloroplast assemblies in crop genetics, breeding, and related agricultural research.

Methodology:

Implemented as a Snakemake workflow that assembles chloroplast genomes from long-read sequencing data and evaluates assemblies against publicly available reference chloroplast genome assemblies.