Long-Read Metagenomic Sequencing

What Is Long-Read Metagenomic Sequencing?

Metagenome long-read sequencing is Psomagen's cutting-edge solution for overcoming the limitations of short-read assembly. By utilizing PacBio Revio, we provide significantly longer reads that span repetitive regions and entire operons, enabling the construction of complete, high-quality metagenome-assembled genomes (MAGs).

Why Is Long-Read Metagenomics Important?

This service is essential for researchers focused on novel microbial discovery, accurate strain phasing, and high resolution complex microbial communities. It moves beyond abundance and potential to deliver a structural, genomic understanding of the microbiome.

What Can You Do?

High-Quality MAGs

Near-complete genome assembly for individual species within the complex mixture, essential for functional validation.

Strain-Level Resolution

Resolves strain variation and structural differences often missed by short-read approaches.

Complex Region Resolution

Long reads effectively span highly repetitive or complex genomic regions (e.g., rRNA operons, prophages).

Choosing a Service

Psomagen offers both high-accuracy HiFi sequencing and full-legnth amplicon sequencing allowing you to choose the platform that best fits your project's needs for quality, speed, or read length. For custom projects, please reach out to schedule a consultation.

	HiFi Long Read	Full Length Amplicon
Target Molecule	Total DNA (high molecular weight)	PCR amplicons (16S full-length)
Platform	PacBio Revio	PacBio Revio
Read Length	10-25 kb HiFi reads	~1.5 kb (full 16S gene)
Primary Goal	Highly accurate long reads for superior MAG quality.	Species/strain-level ID without assembly.
Deliverables	FASTQ, BAM files Analysis results	FASTQ file Analysis results

Preprocessing and QC Measures

Successful long-read sequencing hinges on the quality of the input DNA.

DNA Quality: Requires high-molecular-weight (HMW) DNA with minimal shearing, checked by electrophoresis.
Library Preparation: Optimized protocols to preserve read length.
Multiplexing: Careful attention to pooling and indexing to ensure sufficient depth per sample for robust assembly.

De Novo Assembly and Binning (MAG Generation)

Long reads provide the scaffolding necessary to build complete contigs, which are then used to reconstruct individual microbial genomes.

Assembly: Specialized long-read assembly algorithms are used to generate contiguous sequences.
Binning: Assembled contigs are grouped (binned) based on characteristics (e.g., coverage, GC content) to create individual MAGs.
MAG Quality Check (CheckM): Each MAG is rigorously assessed for completeness (how much of the expected genome is present) and contamination (how much foreign DNA is included). Only high-quality MAGs (e.g. >90% complete, <5% contamination) are reported.

Functional & Comparative Genomics

Once high-quality MAGs are obtained, advanced genomic analysis can be performed at the strain level.

Strain Phasing: The ability to distinguish between closely related strains, crucial for identifying true functional drivers.
Annotation: Complete MAGs are annotated to reveal the full set of metabolic pathways, ARGs, and virulence factors for specific, individual species.
Comparative Genomics: Comparing MAGs from different samples/conditions to identify genetic variations and insertions/deletions (InDels) driving community differences.

Analysis Report and Support

Our long-read reporting focuses on the quality and content of the assembled microbial genomes.

Result Type	File Format	Detailed Content
Raw Data	FASTQ, BAM	Final sequencing data.
Basic Report	HTML, XLSX	Assembly Statistics (N50, Max Contig Length), Binning Summary, MAG Quality Check (CheckM results).
Advanced Report	HTML, FASTA	High-Quality MAGs (FASTA files), MAG Functional Annotation (KEGG/COG), Comparative Genomics Results.

Expert Support

Long-read data requires specialized assembly and binning expertise. Our team excels in complex data processing and MAG validation, offering comprehensive support for your most ambitious projects.

SERVICES // METAGENOMICS