OPERA-MS | OPERA-MS - Hybrid Metagenomic Assembler | Genomics library

OPERA-MS is a C++ library typically used in Artificial Intelligence, Genomics applications. OPERA-MS has no bugs, it has no vulnerabilities and it has low support. However OPERA-MS has a Non-SPDX License. You can download it from GitHub.

OPERA-MS is a hybrid metagenomic assembler which combines the advantages of short and long-read technologies to provide high quality assemblies, addressing issues of low contiguity for short-read only assemblies, and low base-pair quality for long-read only assemblies. OPERA-MS has been extensively tested on mock and real communities sequenced using different long-read technologies, including Oxford Nanopore, PacBio and Illumina Synthetic Long Read, and is particularly robust to noise in the read data. OPERA-MS employs a staged assembly strategy that is designed to exploit even low coverage long read data to improve genome assembly. It begins by constructing a short-read metagenomic assembly (default: MEGAHIT) that provides a good representation of the underlying sequence in the metagenome but may be fragmented. Long and short reads are then mapped to the assembly to identify connectivity between the contigs and to compute read coverage information. This serves as the basis for the core of the OPERA-MS algorithm which is to exploit coverage as well as connectivity information to accurately cluster contigs into genomes using a Bayesian model based approach. Another important advantage of OPERA-MS is that it can deconvolute strains in the metagenome, optionally using information from reference genomes to support this. This is fundamentally challenging for pipelines that begin with assembly of error-prone long reads. After clustering, individual genomes are further scaffolded and gap-filled using the lightweight and robust scaffolder OPERA-LG. OPERA-MS can assemble near complete genomes from a metagenomic dataset with as little as 9x long-read coverage. It is designed to be conservative and avoid aggresive assembly, a strategy favored by many modern assemblers that aim to report high contiguity statistics. Applied to human gut microbiome data, OPERA-MS provides hundreds of high quality draft genomes, a majority of which have N50 >100kbp. We observed the assembly of complete plasmids, many of which were novel and contain previously unseen resistance gene combinations. In addition, OPERA-MS can very accurately assemble genomes even in the presence of multiple strains of a species in a complex metagenome, allowing us to associate plasmids and host genomes using longitudinal data. For further details about these and other results using nanopore sequencing on stool samples from clinical studies see our manuscript or preprint.