CulebrONT

CulebrONT automates genome assembly and evaluation from long-read sequencing data for prokaryotic and eukaryotic genomes.

Key Features:

• Workflow management: Uses Snakemake to provide a scalable, modular, and traceable workflow framework.
• Multiple assembler support: Enables parallel testing across multiple long-read assemblers and samples.
• Downstream processing: Provides optional circularization and polishing steps to improve assembly contiguity and accuracy.
• Assembly quality assessment: Compiles a suite of assembly quality metrics into a report for comparative evaluation.
• Input data: Operates on raw long-read sequencing reads for both prokaryotic and eukaryotic genomes.

Scientific Applications:

• High-quality genome assembly: Producing contiguous assemblies for genomic studies requiring high-quality genomes.
• Complex eukaryotic genome assembly: Handling assembly of complex eukaryotic genomes using long-read data.
• Prokaryotic genome assembly: Assembling diverse prokaryotic species with support for circularization.
• Comparative assembler evaluation: Parallel testing of assemblers and samples to identify optimal assembly configurations.

Methodology:

Uses Snakemake to orchestrate parallel execution of multiple long-read assemblers across samples, performs optional circularization and polishing, and compiles assembly quality metrics into a report.