Improving eukaryotic bins using branchwater metagenomic signatures
To improve the completeness of low-quality eukaryotic bins, we used a k-mer–based search strategy to identify metagenomic samples sharing a high fraction of k-mers with each target bin, using branchwater. These matched samples were then used as input for co-assembly, with the aim of recovering more complete eukaryotic genomes. We began with 235 eukaryotic bins from project ERP137072 and selected those with = 60% completeness, resulting in 32 low-quality bins. Each bin was used as an anchor to query metagenomes through branchwater, retrieving all samples with high containment. In all cases, the original sample from which the bin was generated was recovered. We then focused on bins that had at least one additional metagenomic sample with containment = 1, resulting in three candidate bins suitable for improvement by co-assembly. Raw reads from the selected samples underwent quality control with Fastp v0.23.4, followed by decontamination using bwa-mem2 v2.2.1 and samtools v1.19.2, with the human genome as the reference. Co-assemblies were generated using MEGAHIT v1.2.9. MAGs were generated using the MGnify Genomes Generation Pipeline v1.3.0. This study contains the generated coassemblies and MAGs.