RT Journal Article
SR Electronic
T1 3CAC: improving the classification of phages and plasmids from metagenomic assemblies using assembly graphs
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2021.11.05.467408
DO 10.1101/2021.11.05.467408
A1 Lianrong Pu
A1 Ron Shamir
YR 2021
UL http://biorxiv.org/content/early/2021/11/05/2021.11.05.467408.abstract
AB Bacteriophages and plasmids usually coexist with their host bacteria in microbial communities and play important roles in microbial evolution. Accurately identifying sequence contigs as phages, plasmids, and bacterial chromosomes in mixed metagenomic assemblies is critical for further unravelling their functions. Many classification tools have been developed for identifying either phages or plasmids in metagenomic assemblies. However, only two classifiers, PPR-Meta and viralVerify, were proposed to simultaneously identify phages and plasmids in mixed metagenomic assemblies. Due to the very high fraction of chromosome contigs in the assemblies, both tools achieve high precision in the classification of chromosomes but perform poorly in classifying phages and plasmids. Short contigs in these assemblies are often wrongly classified or classified as uncertain.Here we present 3CAC, a new three-class classifier that improves the precision of phage and plasmid classifications. 3CAC starts with an initial three-class classification generated by existing classifiers and further improves the classification of short contigs and contigs with low confidence classification by using proximity in the assembly graph. Evaluation on simulated metagenomes and on real human gut microbiome samples showed that 3CAC outperformed PPR-Meta and viralVerify in both precision and recall, and increased F1-score by at least 10 percentage points.Competing Interest StatementThe authors have declared no competing interest.