Lathe

Lathe reconstructs high-quality bacterial genomes from human gut metagenomic long-read sequencing data.

Key Features:

• High-Molecular-Weight DNA Extraction: Protocol extracts microgram quantities of high-molecular-weight DNA from human stool samples suitable for long-read sequencing.
• Long-Read Sequencing Compatibility: Optimized for Nanopore long-read sequencing to support contiguous bacterial genome assembly.
• Computational Workflow: Includes long-read basecalling, assembly, consensus refinement using both long reads and Illumina short reads, and genome circularization.
• Efficiency: End-to-end process from DNA extraction to genome assembly reported to complete in approximately 10 days with about 2 days of hands-on bench and computational effort.

Scientific Applications:

• Microbiome genomics: Generation of high-quality contiguous bacterial genomes from human gut metagenomes to support genomic and functional analyses.
• Mobile genetic element analysis: Recovery of repeated genomic elements, including mobile genetic elements, to study their roles in bacterial phenotype, adaptation, and pathogenicity.
• Gene function and diversity studies: Improved assemblies facilitate investigation of microbial diversity and gene function within the gut microbiome.

Methodology:

Long-read basecalling, assembly, consensus refinement using both long reads and Illumina short reads, and genome circularization.