MetaTrass: High-quality metagenome assembly on the human gut microbiome by co-barcoding sequencing reads

Abstract

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.

Assembly and analytical validation of a metagenomic reference catalog of human gut microbiota based on co-barcoding sequencing

“…Although we did not compare the assembly results between the stLFR method and TGS method in this study, previous reports have shown the advantages of the stLFR method over TGS in the application of metagenomics. Compared with ONT, the stLFR method generated more species with an NG50 of around 2M and fewer mismatches and INDELs (Qi et al, 2022). Zhang demonstrated that the assembly results based on stLFR data generated more nearcomplete metagenome-assembled genomes than PacBio long-reads in real fecal samples (Zhang et al, 2022).…”

“…A total of 3,649.41 Gb of highquality data were obtained from 50 samples for further analysis, with an average sample size of 72.99 ± 17.68 Gb (mean ± S.D.). The high-quality reads were assembled using MetaTrass (Qi et al, 2022), developed for metagenomic stLFR library sequencing data, and the assembled genomes were quantified using CheckM v1.1.2 (Parks et al, 2015). To eliminate redundant high-quality genomes, dRep v3.2.0 (Olm et al, 2017) was employed to construct a catalog of reference genomes, with parameters set to "-pa 0.9 -sa 0.95nc 0.6 -cm larger."…”