Hybrid De Novo Genome Assembly Using MiSeq and SOLiD Short Read Data

Area of Science:

• Genomics
• Bioinformatics
• Computational Biology

Background:

• De novo genome assembly is crucial for understanding microbial genomes.
• Short-read sequencing technologies offer high accuracy but can struggle with complex genomic structures.
• Integrating diverse sequencing data can overcome individual technology limitations.

Purpose of the Study:

• To develop and evaluate a hybrid de novo assembly pipeline using both MiSeq and SOLiD short read data.
• To assess the impact of combining different sequencing data types on assembly quality.
• To improve the accuracy and completeness of genome assemblies, particularly for gene-rich regions.

Main Methods:

• A hybrid de novo assembly pipeline was constructed, incorporating ABySS and SOAPdenovo.
• The pipeline accepted MiSeq paired-end and SOLiD mate-paired data, individually or combined.
• Assembly performance was evaluated by aligning results to reference genomes of Aspergillus oryzae and Streptomyces avermitilis.

Main Results:

• Hybrid assembly using both MiSeq and SOLiD data improved alignment length by 3-8 fold for A. oryzae compared to single-data assemblies.
• The number of reproduced secondary metabolite biosynthesis gene clusters increased with hybrid assembly.
• For S. avermitilis, hybrid assembly improved alignment length by 2-fold, even with low-quality SOLiD data.

Conclusions:

• Combining MiSeq and SOLiD data in a hybrid assembly pipeline enhances genome assembly accuracy and contiguity.
• MiSeq data's long reads are vital for nucleotide sequence precision.
• SOLiD mate-paired reads with long insertion lengths aid in long-range sequence arrangement, improving overall assembly.
• This hybrid approach is effective even for challenging genomes like high-GC content bacteria.