Unknown

Dataset Information

0

GUNC: detection of chimerism and contamination in prokaryotic genomes.


ABSTRACT: Genomes are critical units in microbiology, yet ascertaining quality in prokaryotic genome assemblies remains a formidable challenge. We present GUNC (the Genome UNClutterer), a tool that accurately detects and quantifies genome chimerism based on the lineage homogeneity of individual contigs using a genome's full complement of genes. GUNC complements existing approaches by targeting previously underdetected types of contamination: we conservatively estimate that 5.7% of genomes in GenBank, 5.2% in RefSeq, and 15-30% of pre-filtered "high-quality" metagenome-assembled genomes in recent studies are undetected chimeras. GUNC provides a fast and robust tool to substantially improve prokaryotic genome quality.

SUBMITTER: Orakov A 

PROVIDER: S-EPMC8201837 | biostudies-literature | 2021 Jun

REPOSITORIES: biostudies-literature

altmetric image

Publications

GUNC: detection of chimerism and contamination in prokaryotic genomes.

Orakov Askarbek A   Fullam Anthony A   Coelho Luis Pedro LP   Khedkar Supriya S   Szklarczyk Damian D   Mende Daniel R DR   Schmidt Thomas S B TSB   Bork Peer P  

Genome biology 20210613 1


Genomes are critical units in microbiology, yet ascertaining quality in prokaryotic genome assemblies remains a formidable challenge. We present GUNC (the Genome UNClutterer), a tool that accurately detects and quantifies genome chimerism based on the lineage homogeneity of individual contigs using a genome's full complement of genes. GUNC complements existing approaches by targeting previously underdetected types of contamination: we conservatively estimate that 5.7% of genomes in GenBank, 5.2%  ...[more]

Similar Datasets

| S-EPMC9336565 | biostudies-literature
| S-EPMC10831095 | biostudies-literature
| S-EPMC4547308 | biostudies-literature
| S-EPMC1458513 | biostudies-literature
| S-EPMC3488263 | biostudies-literature
| S-EPMC3282942 | biostudies-literature
| S-EPMC1895974 | biostudies-literature
| S-EPMC1347423 | biostudies-literature
| S-EPMC2362131 | biostudies-literature
| S-EPMC3098052 | biostudies-literature