MetaTrass: High-quality Metagenomic Taxonomic Read Assembly of Single-Species based on co-barcoding sequencing data and references

With the development of sequencing technologies and computational analysis in metagenomics, the genetic diversity of non-conserved region has been receiving increasing attention to unravel complex microbial communities. However, it remains a challenge to obtain enough microbial genome drafts at a high resolution from a microbial community sample. In this work, we presented MetaTrass, a reference-guided assembling pipeline, which exploited both the public microbe reference genomes and long-range co-barcoding information, to assemble high-quality draft genomes from metagenomic co-barcoding reads. By applying this approach to single tube long fragment reads (stLFR) datasets of four human faeces samples, MetaTrass could generate more high-quality genome drafts (>90% completeness, <5%contamination) with longer contiguity and higher resolution in comparison with the common combination strategies of genome assembling and binning. Total of 178 high-quality genomes were assembled by MetaTrass, comparing to 58 high-quality genomes assembled by the combination strategies. These high-quality genomes paved the way of the genetic diversity and evolution analysis among different samples. Thus, MetaTrass will facilitate the study of spatial and dynamics of complex microbial communities at high resolution. The open-source code of MetaTrass is available at https://github.com/BGI-Qingdao/MetaTrass.