GUNC: detection of chimerism and contamination in prokaryotic genomes

Orakov, Askarbek; Fullam, Anthony; Coelho, Luís Pedro; Khedkar, Supriya; Szklarczyk, Damian; Mende, Daniel; Schmidt, Thomas; Bork, Peer

doi:10.1186/s13059-021-02393-0

Cited by 156 publications

(136 citation statements)

References 52 publications

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“…As MAGs are not always submitted to INSDC repositories, we are exploring incorporation of additional repositories into the GTDB such as MGnify ( 38 ). The quality of MAGs is an ongoing concern and we are evaluating methods for decontaminating MAGs ( 39 ) and identifying and removing MAGs that may contribute to phylogenetic instability ( 40 ). Related to MAG quality, we expect to change the AF criteria used for assigning genomes to GTDB species clusters from 0.65 to 0.5 starting in the next GTDB release in order to better accommodate the growing number of incomplete MAGs contained in the GTDB which can cause the AF between MAGs to be artificially low.…”

Section: Concluding Remarks and Future Plansmentioning

confidence: 99%

GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy

Parks

Chuvochina

Rinke

et al. 2021

Nucleic Acids Research

1,164

832

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The Genome Taxonomy Database (GTDB; https://gtdb.ecogenomic.org) provides a phylogenetically consistent and rank normalized genome-based taxonomy for prokaryotic genomes sourced from the NCBI Assembly database. GTDB R06-RS202 spans 254 090 bacterial and 4316 archaeal genomes, a 270% increase since the introduction of the GTDB in November, 2017. These genomes are organized into 45 555 bacterial and 2339 archaeal species clusters which is a 200% increase since the integration of species clusters into the GTDB in June, 2019. Here, we explore prokaryotic diversity from the perspective of the GTDB and highlight the importance of metagenome-assembled genomes in expanding available genomic representation. We also discuss improvements to the GTDB website which allow tracking of taxonomic changes, easy assessment of genome assembly quality, and identification of genomes assembled from type material or used as species representatives. Methodological updates and policy changes made since the inception of the GTDB are then described along with the procedure used to update species clusters in the GTDB. We conclude with a discussion on the use of average nucleotide identities as a pragmatic approach for delineating prokaryotic species.

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Section: Concluding Remarks and Future Plansmentioning

confidence: 99%

GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy

Parks

Chuvochina

Rinke

et al. 2021

Nucleic Acids Research

1,164

832

View full text Add to dashboard Cite

show abstract

“…There remains an urgent need for methods to identify non–cognate contigs in fractionated assemblies, with the impact of contamination on gene–level becoming more widely recognised (Arkhipova, 2020), and one recently published analysis suggests that up to 15–30% of publicly–available MAGs classified at pHQ level will harbour chimeric content (Orakov et al, 2021). In the present study, we have examined removal of possible contamination using the RefineM workflow (Parks et al, 2017).…”

Section: Discussionmentioning

confidence: 99%

Recovery of high quality metagenome–assembled genomes from full–scale activated sludge microbial communities in a tropical climate using longitudinal metagenome sampling

Haryono

Law

Arumugam

et al. 2021

Preprint

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Analysis of metagenome data based on the recovery of draft genomes (so called metagenome-assembled genomes, or MAG) have assumed an increasingly central role in microbiome research in recent years. Microbial communities underpinning the operation of wastewater treatment plants are particularly challenging targets for MAG analysis due to their high ecological complexity, and remain important, albeit understudied, microbial communities that play a key role in mediating interactions between human and natural ecosystems. In this paper, we consider strategies for recovery of MAG sequence from time series metagenome surveys of full-scale activated sludge microbial communities. We generate MAG catalogues from this set of data using several different strategies, including the use of multiple individual sample assemblies, two variations on multi-sample co-assembly and a recently published MAG recovery workflow using deep learning. We obtain a total of just under 9,100 draft genomes, which collapse to around 3,100 non-redundant genomic clusters. We examine the strengths and weaknesses of these approaches in relation to MAG yield and quality, showing the co-assembly offers clear advantages over single-sample assembly. Around 1000 MAGs were candidates for being considered high quality, based on single-copy marker gene occurrence statistics, however only 58 MAG formally meet the MIMAG criteria for being high quality draft genomes. These findings carry broader implications for performing genome-resolved metagenomics on highly complex communities, the design and implementation of genome recoverability strategies, MAG decontamination and the search for better binning methodology.

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“…MAGpurify [10] removes scaffolds that are far from those from the same MAG by considering information from multiple sources, such as phylogenetic marker genes, clade-specific markers and GC content. GUNC [145] calculates the clade separation and reference representation scores to quantify genomic chimerism. The construction of MAGs should ideally be performed for all of the high-, medium- and low-abundance microbes.…”

Section: Outlook Potential Challenges and Strategies To Address Themmentioning

confidence: 99%

A review of computational tools for generating metagenome-assembled genomes from metagenomic sequencing data

Yang

Chowdhury

Zhang

et al. 2021

Computational and Structural Biotechnology Journal

135

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GUNC: detection of chimerism and contamination in prokaryotic genomes

Cited by 156 publications

References 52 publications

GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy

GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy

Recovery of high quality metagenome–assembled genomes from full–scale activated sludge microbial communities in a tropical climate using longitudinal metagenome sampling

A review of computational tools for generating metagenome-assembled genomes from metagenomic sequencing data

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