Exploring high-quality microbial genomes by assembling short-reads with long-range connectivity

Exploring high-quality microbial genomes by assembling short-reads with long-range connectivity

Blog Article

Abstract Although long-read sequencing enables the generation of complete genomes for unculturable microbes, its high cost limits the widespread adoption of long-read sequencing in large-scale metagenomic studies.An alternative method is to assemble short-reads with long-range connectivity, which can be a cost-effective way to generate high-quality microbial genomes.Here, we develop Pangaea, a bioinformatic approach designed to enhance metagenome assembly using short-reads with long-range Venting Kit connectivity.Pangaea leverages connectivity derived from physical barcodes of linked-reads or virtual barcodes by aligning short-reads to long-reads.

Pangaea utilizes a deep learning-based read binning algorithm to assemble co-barcoded reads exhibiting similar sequence contexts and Gift Wrap abundances, thereby improving the assembly of high- and medium-abundance microbial genomes.Pangaea also leverages a multi-thresholding algorithm strategy to refine assembly for low-abundance microbes.We benchmark Pangaea on linked-reads and a combination of short- and long-reads from simulation data, mock communities and human gut metagenomes.Pangaea achieves significantly higher contig continuity as well as more near-complete metagenome-assembled genomes (NCMAGs) than the existing assemblers.

Pangaea also generates three complete and circular NCMAGs on the human gut microbiomes.