Reference-guided assembly of metagenomes with MetaCompass

Tu Luan; Victoria P Cepeda-Espinoza; Bo Liu; Zac Bowen; Ujjwal Ayyangar; Mathieu Almeida; Sergey Koren; Todd J Treangen; Adam Porter; Mihai Pop

doi:10.1016/j.crmeth.2025.101186

Reference-guided assembly of metagenomes with MetaCompass

Cell Rep Methods. 2025 Oct 20;5(10):101186. doi: 10.1016/j.crmeth.2025.101186. Epub 2025 Sep 26.

Authors

Affiliations

¹ Department of Computer Science, University of Maryland, College Park, MD 20742, USA; Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA.
² Fraunhofer USA Center Mid-Atlantic, Riverdale, MD 20737, USA.
³ Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA.
⁴ Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, Bethesda, MD 20892, USA.
⁵ Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA; Department of Computer Science, Rice University, Houston, TX 77005, USA.
⁶ Department of Computer Science, University of Maryland, College Park, MD 20742, USA.
⁷ Department of Computer Science, University of Maryland, College Park, MD 20742, USA; Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA. Electronic address: mpop@umd.edu.

Abstract

Metagenomic studies have primarily relied on de novo assembly for reconstructing genes and genomes from microbial mixtures. While reference-guided approaches have been employed in the assembly of single organisms, they have not been used in a metagenomic context. Here, we develop an effective approach for reference-guided metagenomic assembly that can complement and improve upon de novo metagenomic assembly methods for certain organisms. Such approaches will be increasingly useful as more genomes are sequenced and made publicly available.

Keywords: CP: genetics; CP: microbiology; comparative assembly; metagenome assembly; metagenomics; microbiome; reference-guided assembly.

MeSH terms

Humans
Metagenome* / genetics
Metagenomics* / methods
Sequence Analysis, DNA / methods
Software*

Abstract

MeSH terms

Grants and funding