High-resolution metagenome assembly for modern long reads with myloasm

2025/09/06 by Jim Shaw, Maximillian G. Marin, Heng Li · 1 voice · 2 citations
Biochemistry, Genetics and Molecular Biology · Environmental Science · #Bacteriophages and microbial interactions #Genomics and Phylogenetic Studies #Microbial Community Ecology and Physiology

paper · pdf · doi:10.1101/2025.09.05.674543

openalex publication_date 2025/09/06 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/22

Abstract

Long-read metagenome assembly promises complete genomic recovery from microbiomes. However, the complexity of metagenomes poses challenges. We present myloasm, a metagenome assembler for PacBio HiFi and Oxford Nanopore Technologies (ONT) R10.4 long reads. Myloasm uses polymorphic k-mers to construct a high-resolution string graph and then leverages differential abundance for graph simplification. On real-world ONT metagenomes, myloasm assembled three times more complete circular contigs than the next-best assembler. Myloasm can make ONT and HiFi comparable for assembly: for a jointly sequenced gut metagenome, myloasm with ONT assembled more complete circular genomes than any assembler with HiFi. Myloasm recovers previously inaccessible within-species diversity; we recovered six complete Prevotella copri single-contig genomes from a gut metagenome and eight complete TM7 (Saccharibacteria) contigs with > 93% similarity from an oral metagenome. With this improved resolution, we resolved two 98% similar ermF antibiotic resistance genes spreading through distinct strain-specific mobile genetic elements in a human gut.

Citations

• Efficient near-telomere-to-telomere assembly of nanopore simplex reads
• Efficient near telomere-to-telomere assembly of Nanopore Simplex reads
• Culture-independent meta-pangenomics enabled by long-read metagenomics reveals associations with pediatric undernutrition
• Gut microbiota strain richness is species specific and affects engraftment
• High-quality metagenome assembly from long accurate reads with metaMDBG
• Identification of mobile genetic elements with geNomad
• Oenologues, qui êtes-vous?
• CARD 2023: expanded curation, support for machine learning, and resistome prediction at the Comprehensive Antibiotic Resistance Database
• CheckM2: a rapid, scalable and accurate tool for assessing microbial genome quality using machine learning
• Bakta: rapid and standardized annotation of bacterial genomes via alignment-free sequence identification
• Metagenome assembly of high-fidelity long reads with hifiasm-meta
• The complete sequence of a human genome
• Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation
• Haplotype-resolved de novo assembly with phased assembly graphs
• Optimal Assembly for High Throughput Shotgun Sequencing

Cited by

• Fast and haplotype-aware assembly of high-fidelity reads based on MSR sketching: the Alice assembler
• The Microflora Danica atlas of Danish environmental microbiomes
• High-quality metagenome assembly from nanopore reads with nanoMDBG

Discussions

• Jim Shaw @jimshaw.bsky.social presented "High-resolution metagenome assembly for modern long reads with myloasm" This efficient tool uses SNPmers and leverages high quality ONT and PacBio reads for me [bsky, 3 points, 1 comments]

Related

• High-quality metagenome assembly from long accurate reads with metaMDBG
• Metagenome assembly of high-fidelity long reads with hifiasm-meta
• High-quality metagenome assembly from nanopore reads with nanoMDBG
• Towards complete representation of bacterial contents in metagenomic samples
• Fast and haplotype-aware assembly of high-fidelity reads based on MSR sketching: the Alice assembler