Unicycler

Unicycler assembles bacterial genomes by performing hybrid assembly of Illumina short reads together with Pacific Biosciences and Oxford Nanopore Technologies long reads to produce accurate, contiguous assemblies.

Key Features:

• Hybrid Assembly Approach: Integrates Illumina short reads with Pacific Biosciences and Oxford Nanopore long reads to leverage short-read accuracy and long-read structural resolution.
• Initial Assembly Graph Construction: Constructs an initial assembly graph from short reads using the de novo assembler SPAdes to establish an accurate foundational assembly.
• Graph Simplification and Long-Read Alignment: Simplifies the short-read assembly graph by incorporating information from both short and long reads and aligns long reads to the graph using a novel semi-global aligner.
• Performance and Efficiency: Comparative tests on synthetic and real datasets report larger contigs with fewer misassemblies than other hybrid assemblers, including under conditions of low long-read depth and accuracy.
• Cost-Effectiveness: Combines the complementary strengths of short- and long-read sequencing to provide a cost-effective approach for bacterial genome assembly.

Scientific Applications:

• Microbial Genomics: Produces high-quality bacterial genome assemblies for analyses of antibiotic resistance, virulence factors, and microbial ecology.
• Comparative Genomics: Enables comparison of bacterial genomes to identify evolutionary relationships and functional genomic differences.
• Metagenomics: Improves assembly of bacterial genomes from complex environmental or clinical samples containing multiple species.

Methodology:

Constructs an initial assembly graph with SPAdes from short reads, simplifies the graph by incorporating short- and long-read information, and aligns long reads to the assembly graph using a novel semi-global aligner.