Introduction

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 works with:

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

Installation and Usage: See the Install and Usage sections on the navigation side bar. Source code is available at the GitHub repo.

Why myloasm?

Results: Here are some preliminary results for myloasm until the preprint officially comes out.

Philosophy: Myloasm was designed to take advantage of modern long reads. Even the noisiest modern long reads (e.g., nanopore simplex R10) have become quite accurate—myloasm uses a new approach that enables high-resolution assembly from this data.

Strengths: myloasm can

• often assemble similar (intraspecies) strains better than other nanopore assemblers
• take advantage of very long reads better than de Bruijn graph approaches
• obtain contiguous assemblies in even complex, highly heterogeneous metagenomes

Limitations: myloasm may

• occasionally produce chimeric misassembled contigs due to its aggressiveness.
  • we provide extra debugging information for manual curation; see the quality control guide.
• use more memory than other assemblers. Currently, a ~200 gigabase long-read human gut sample takes ~450 GB of RAM.

Issues, questions, and discussions

• Found a bug or have an issue? Go to https://github.com/bluenote-1577/myloasm/issues
• Have a general question or discussion topic? Go to https://github.com/bluenote-1577/myloasm/discussions

Citation

Jim Shaw and Heng Li. Forthcoming.