metaMIC manuscript by Senying Lai et al. out at GenomeBiology!
Can we identify missassembled contigs? Can we fix them?
Not always, but often yes
Looking at read mappings and sequence features, we can identify situations where the assemblers got it wrong
Missassembled contigs are relatively rare, but binning corrected contigs leads to a 10-20% in the number of high-quality bins obtained
https://genomebiology.biomedcentral.com/articles/10.1186/s13059-022-02810-y
metaMIC: reference-free misassembly identification and correction of de novo metagenomic assemblies - Genome Biology
Evaluating the quality of metagenomic assemblies is important for constructing reliable metagenome-assembled genomes and downstream analyses. Here, we present metaMIC ( https://github.com/ZhaoXM-Lab/metaMIC ), a machine learning-based tool for identifying and correcting misassemblies in metagenomic assemblies. Benchmarking results on both simulated and real datasets demonstrate that metaMIC outperforms existing tools when identifying misassembled contigs. Furthermore, metaMIC is able to localize the misassembly breakpoints, and the correction of misassemblies by splitting at misassembly breakpoints can improve downstream scaffolding and binning results.