RT Journal Article
SR Electronic
T1 MIDAS2: Metagenomic Intra-species Diversity Analysis System
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2022.06.16.496510
DO 10.1101/2022.06.16.496510
A1 Chunyu Zhao
A1 Boris Dimitrov
A1 Miriam Goldman
A1 Stephen Nayfach
A1 Katherine S. Pollard
YR 2022
UL http://biorxiv.org/content/early/2022/06/17/2022.06.16.496510.abstract
AB 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 (CNVs) 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. The documentation is available at https://midas2.readthedocs.io/en/latest/.Supplementary Information Supplementary data are available at Bioinformatics online.Competing Interest StatementThe authors have declared no competing interest.