Metagenomic assemblies tend to break around antibiotic resistance genes
Our study shows that metaSPAdes and Trinity would be the preferable tools in terms of accuracy to recover correct genomic contexts around ARGs in metagenomic samples characterized by uneven coverages. Overall, the inability of assemblers to reconstruct long ARG-containing contigs has impacts on ARG quantification, suggesting that directly mapping reads to an ARG database should be performed as a complementary strategy to get accurate ARG abundance and diversity measures.
Authors
- Anna Abramova (ORCID: https://orcid.org/0000-0002-0493-7808)
- Antti Karkman (ORCID: https://orcid.org/0000-0003-0983-3319)
- Johan Bengtsson‐Palme (ORCID: https://orcid.org/0000-0002-6528-3158)
Institutions
- University of Helsinki (FI)
- Science for Life Laboratory (SE)
- CNR de la Résistance aux Antibiotiques (FR)
- Chalmers University of Technology (SE)
- University of Gothenburg (SE)
Publication Details
- Journal
- BMC Genomics
- Published
- 2024-10-14
- DOI
- https://doi.org/10.1186/s12864-024-10876-0
- Citations
- 35
- Primary Topic
- Genomics and Phylogenetic Studies
- Type
- article
- Field-Weighted Citation Impact
- 8.18
Funders
- Joint Programming Initiative on Antimicrobial Resistance
- Insamlingsstiftelsen Cancer- och Allergifonden
- Stiftelsen för Strategisk Forskning
- Chalmers Tekniska Högskola
- Knut och Alice Wallenbergs Stiftelse
- Vetenskapsrådet
- Göteborgs Universitet
- Sahlgrenska Akademin
- Centre for Antibiotic Resistance Research, University of Gothenburg