w2rap-contigger

w2rap-contigger assembles contigs from Illumina paired-end whole-genome shotgun short reads to produce de novo genome assemblies for large and complex genomes, including polyploid and hexaploid species.

Key Features:

• Robust assembly focus: Emphasizes assembly robustness by optimizing for coverage and short-range contiguity rather than solely maximizing contiguity metrics.
• Illumina paired-end support: Processes low-cost Illumina short reads, including paired-end (PE) data, for whole-genome shotgun assembly.
• Complete assembly stages: Implements stages from data processing through quality control (QC) and scaffolding as part of the assembly workflow.
• Metric-guided optimization: Uses a metric-guided strategy to tune assembly parameters to balance cost-effectiveness and assembly accuracy.
• Polyploid genome capability: Applied to large polyploid crop species and hexaploid genomes to generate de novo assemblies.
• Cross-taxon use: Demonstrated on both plant and human Illumina datasets for de novo assembly tasks.

Scientific Applications:

• De novo assembly of complex genomes: Produces genome assemblies for large, repetitive, or polyploid genomes, including hexaploid species.
• Comparative genomics: Generates assemblies suitable for comparative analyses of genetic diversity and evolutionary relationships.
• Agricultural genomics: Enables rapid, cost-effective de novo assembly of crop genomes for breeding and genomic characterization.

Methodology:

Performs de novo whole-genome shotgun assembly from Illumina paired-end short reads and includes quality control (QC) and scaffolding, using a metric-guided strategy that prioritizes coverage and short-range contiguity.