MIDAS2: Metagenomic Intra-species Diversity Analysis System

Chunyu Zhao; Boris Dimitrov; Miriam Goldman; Stephen Nayfach; Katherine S Pollard

doi:10.1093/bioinformatics/btac713

MIDAS2: Metagenomic Intra-species Diversity Analysis System

Bioinformatics. 2023 Jan 1;39(1):btac713. doi: 10.1093/bioinformatics/btac713.

Authors

Chunyu Zhao^{1

2}, Boris Dimitrov³, Miriam Goldman^{2

4}, Stephen Nayfach^{5

6}, Katherine S Pollard^{1

2

7}

Affiliations

¹ Data Science, Chan Zuckerberg Biohub, San Francisco, CA 94158, USA.
² Gladstone Institute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA 94158, USA.
³ Chan Zuckerberg Initiative, Redwood City, CA 94063, USA.
⁴ Biomedical Informatics Graduate Program, University of California San Francisco, San Francisco, CA 94158, USA.
⁵ Department of Energy, Joint Genome Institute, Berkeley, CA 94720, USA.
⁶ Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
⁷ Department of Epidemiology and Biostatistics, University of California, San Francisco, CA 94158, USA.

Abstract

Summary: The Metagenomic Intra-Species Diversity Analysis System (MIDAS) is a scalable metagenomic pipeline that identifies single nucleotide variants (SNVs) and gene copy number variants in microbial populations. Here, we present MIDAS2, which addresses the computational challenges presented by increasingly large reference genome databases, while adding functionality for building custom databases and leveraging paired-end reads to improve SNV accuracy. This fast and scalable reengineering of the MIDAS pipeline enables thousands of metagenomic samples to be efficiently genotyped.

Availability and implementation: The source code is available at https://github.com/czbiohub/MIDAS2.

Supplementary information: Supplementary data are available at Bioinformatics online.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Databases, Factual
Genotype
Metagenome*
Metagenomics
Software*

Abstract

Publication types

MeSH terms

Grants and funding