pilon

pilon corrects de novo genome assemblies and calls sequence variants to improve assembly accuracy and detect small and large variants in bacterial and other genomes.

Key Features:

• Automated Assembly Correction: Automatically fixes bases, resolves mis-assemblies, and fills gaps in draft genome assemblies to produce more contiguous genomes with reduced errors.
• Variant Calling Capabilities: Identifies both small variants with high accuracy and larger structural events including insertions, deletions, and duplications.
• Compatibility with Diverse Sequencing Data: Operates with multiple sequencing data types and performs optimally with paired-end Illumina data from two libraries, e.g., short inserts (~180 bp) and larger inserts (~3–5 Kb).
• Support for Haploid and Diploid Genomes: Applies assembly improvement and variant detection to both haploid and diploid genomes to enhance gene identification and assembly accuracy.

Scientific Applications:

• Bacterial Genome Assembly Refinement: Used to refine de novo assemblies of bacterial genomes, improving contiguity and accuracy for downstream analyses.
• Variant Discovery in Clinical Strains: Employed to identify sequence variants across clinically relevant bacterial strains to support studies of microbial genetics and pathogenesis.

Methodology:

Performs automated correction of draft assemblies by fixing bases, resolving mis-assemblies, and filling gaps, and calls small and large sequence variants from sequencing data, particularly leveraging paired-end Illumina libraries with short (~180 bp) and longer (3–5 Kb) inserts.