Recovery and Analysis of Long-Read Metagenome-Assembled Genomes

Krithika Arumugam; Irina Bessarab; Mindia A S Haryono; Rohan B H Williams

doi:10.1007/978-1-0716-3072-3_12

Recovery and Analysis of Long-Read Metagenome-Assembled Genomes

Methods Mol Biol. 2023:2649:235-259. doi: 10.1007/978-1-0716-3072-3_12.

Authors

Krithika Arumugam¹, Irina Bessarab², Mindia A S Haryono², Rohan B H Williams³

Affiliations

¹ Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore.
² Singapore Centre for Environmental Life Sciences Engineering, National University of Singapore, Singapore, Singapore.
³ Singapore Centre for Environmental Life Sciences Engineering, National University of Singapore, Singapore, Singapore. lsirbhw@nus.edu.sg.

PMID: 37258866
DOI: 10.1007/978-1-0716-3072-3_12

Abstract

The development of long-read nucleic acid sequencing is beginning to make very substantive impact on the conduct of metagenome analysis, particularly in relation to the problem of recovering the genomes of member species of complex microbial communities. Here we outline bioinformatics workflows for the recovery and characterization of complete genomes from long-read metagenome data and some complementary procedures for comparison of cognate draft genomes and gene quality obtained from short-read sequencing and long-read sequencing.

Keywords: Genome refinement; Long-read sequencing; Metagenome assembly; Metagenomics; Microbiome; MinION; Nanopore sequencing.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Base Sequence
High-Throughput Nucleotide Sequencing / methods
Metagenome*
Metagenomics / methods
Microbiota* / genetics
Sequence Analysis, DNA / methods