BinaRena: a dedicated interactive platform for human-guided exploration and binning of metagenomes

Abstract

Exploring metagenomic contigs and "binning" them are essential for delineating functional and evolutionary guilds within microbial communities. Despite available automated binners, researchers often find human involvement necessary to achieve representative results. We present BinaRena, an interactive graphic interface dedicated to aiding human operators to explore contigs via customizable visualization and to associate them with bins based on various data types, including sequence metrics, coverage profiles, taxonomic assignments and functional annotations. Binning plans can be edited, inspected and compared visually or using algorithms. Completeness and redundancy of user-selected contigs can be calculated real-time. We show that BinaRena facilitated biological pattern discovery, hypothesis generation and bin refinement in a tropical peatland metagenome. It enabled isolation of pathogenic genomes within closely-related populations from human gut samples. It significantly improved overall binning quality after curation using a simulated marine dataset. BinaRena is an installation-free, client-end web application for researchers of all levels.

Approximate Nearest Neighbor Graph Provides Fast and Efficient Embedding with Applications in Large-scale Biological Data

“…New metagenomic binning algorithms such as Rosella (Newell, 2023), BinArena (Pavia, et al, 2023), mmgenomes (Karst, et al, 2016) relies on UMAP or t-SNE for visualization of contigs after obtaining the composition of contigs (e.g., Euclidean distance based on kmer composition of contigs) to avoid all versus all distance computation. Then contigs will be manually binned via human intuition or clustering algorithms.…”

Recovery of novel microbial genomes

“…Furthermore, in some cases, automated binning might be insufficient, and hence manual MAG refinement or contig picking may be required, for which various software packages to visualize MAG and contig features have been developed (e.g. mmgenome 96 , Anvi'o 97 , BinaRena 98 , uBin 99 ). If the objective is improving MAG contiguity, reads for genome bins can be extracted and re-assembled using fine-tuned assembly settings to achieve less fragmented or even closed, circular MAGs 45,100 .…”