polishCLR

polishCLR polishes PacBio continuous long read (CLR) genome assemblies by integrating short-read data and iterative polishing to reduce sequencing errors and improve assembly accuracy.

Key Features:

• Nextflow implementation: The workflow is implemented in Nextflow to enable reproducible and scalable execution.
• Reproducibility and best practices: Adheres to Vertebrate Genome Project (VGP) Assembly community best practices for polishing non-model de novo assemblies.
• Input flexibility: Supports multiple input configurations and suboptimal cases to accommodate varying data availability and assembly states.
• Modular design with re-entry points: Allows re-entry at multiple workflow stages, including iterative polishing and evaluation.
• Duplicate haplotype handling: Identifies and removes duplicate haplotypes using purge_dups.
• Optional scaffolding breaks: Provides an option to perform scaffolding breaks when additional data are available.
• Iterative polishing and evaluation: Performs multiple rounds of polishing and evaluation using Arrow and FreeBayes for error correction.
• Containerization: The workflow is containerized to provide consistent computational environments.

Scientific Applications:

• Assembly polishing for PacBio CLR: Improves base-level accuracy of assemblies generated from PacBio CLR data.
• Downstream genomic analyses: Produces higher-quality assemblies that support analyses in evolutionary biology and medical genomics.

Methodology:

Implemented in Nextflow, the workflow integrates short-read data for iterative polishing using Arrow and FreeBayes, includes duplicate-haplotype identification and removal with purge_dups, supports optional scaffolding breaks, and performs multiple rounds of polishing and evaluation within containerized environments.