WENGAN

WENGAN assembles genomes by integrating Oxford Nanopore Technologies (ONT) PromethION, Pacific Biosciences (PacBio) Sequel, Illumina, and MGI sequencing data to produce high-contiguity, high-consensus-quality assemblies of large, repeat-rich genomes.

Key Features:

• Hybrid Assembly Approach: Combines long-read (ONT PromethION, PacBio Sequel) and short-read (Illumina, MGI) data to improve assembly contiguity and consensus quality.
• Efficient Algorithms: Implements algorithms that maximize sequence information from different read types and avoids reliance on all-vs-all read comparisons.
• High-Quality Assemblies: Produces contig NG50 values from 16.67 Mb to 62.06 Mb, contig NGA50 values from 10.9 Mb to 45.91 Mb, consensus QV scores of 27.79 to 33.61, and BUSCO complete metrics between 94.6% and 95.1%.
• Computational Efficiency: Requires between 153 and 1027 CPU hours for assembly tasks.
• Benchmarking Success: Assembled the haploid CHM13 sample with contig NG50 of 62.06 Mb and NGA50 of 45.91 Mb, exceeding the contig NG50 of GRCh38 (57.88 Mb).

Scientific Applications:

• De novo genome assembly: Enables de novo assembly of large, repeat-rich genomes using hybrid sequencing data.
• Human and complex genome assembly: Applied to human samples (including CHM13) to improve contiguity and consensus quality of assemblies.
• Genomics research and reference improvement: Supports generation and benchmarking of high-quality assemblies for comprehensive genomic studies and reference genome improvement.

Methodology:

Integrates ONT PromethION, PacBio Sequel, Illumina, and MGI reads in a hybrid assembly using algorithms that maximize information from different read types and avoid all-vs-all read comparisons.