USDA PacBio Second Pilon Indels Only: Polished Genome Assembly

A genome assembly file produced from PacBio long-read sequencing data. The assembly was performed using Canu and subsequently polished using Illumina short-read data via the Pilon tool, focusing on indel corrections. The dataset was contributed by author Sergey Koren and is hosted on the Papers with Code platform under an Open Access license.

Use Cases

• Benchmarking genome assembly and polishing pipelines based on the described PacBio and Illumina hybrid approach.
• Analyzing the impact of Pilon polishing on indel correction in long-read assemblies based on the description.
• Training or evaluating variant calling models for indel detection using the polished assembly as a reference.

Strengths

• Assembly process is described, involving PacBio long-reads and Illumina short-read polishing via Pilon.
• Data is available under an Open Access license, facilitating reuse.

Limitations

• Description metadata is limited; actual data quality requires manual inspection after download.
• Column-level documentation is absent; field semantics must be inferred after download.
• Row count is unknown, which may limit suitability assessment.

Provenance

Source

Sergey Koren

Collection Method

PacBio assembly via Canu + Illumina Pilon polishing