Myloasm is a de novo metagenome assembler for long-read sequencing data. It takes sequencing reads and outputs polished contigs in a single command. Myloasm uses a novel algorithm that excels for modern long reads, assembling > 2-10 times more circular contigs than metaFlye.

Myloasm works with modern long reads such as:

• Nanopore R10 simplex reads with > ~97% accuracy (basecalled in sup or hac mode)
• PacBio HiFi reads

See the documentation for more information.

Jim Shaw, Maximillian Marin, and Heng Li. High-resolution metagenome assembly for modern long reads with myloasm. Nature Biotechnology (2026).