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| Item Type: | Article |
|---|---|
| Title: | GUNC: detection of chimerism and contamination in prokaryotic genomes |
| Creators Name: | Orakov, A., Fullam, A., Coelho, L.P., Khedkar, S., Szklarczyk, D., Mende, D.R., Schmidt, T.S.B. and Bork, P. |
| 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. |
| Keywords: | Genome Quality, Genome Contamination, Metagenomics, Metagenome-Assembled Genomes, Bioinformatics |
| Source: | Genome Biology |
| ISSN: | 1474-760X |
| Publisher: | BioMed Central |
| Volume: | 22 |
| Number: | 1 |
| Page Range: | 178 |
| Date: | 13 June 2021 |
| Official Publication: | https://doi.org/10.1186/s13059-021-02393-0 |
| PubMed: | View item in PubMed |
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