CoSAG-nf: a scalable nextflow pipeline for co-assembly, optimization, and interactive visualization of high-throughput single-cell genomes.

CoSAG-nf automates high-throughput co-assembly and optimization of single-cell genomes, significantly improving genome quality from highly fragmented SAGs.

• Why it matters: Understanding microbial dark matter and intra-population heterogeneity requires high-quality genomes, but current methods struggle with contamination and fragmentation, limiting scientific insights.
• What they did: The pipeline uses nf-core standards, alignment-free clustering, tetranucleotide profiling, and quality assessment to select optimal SAG combinations, processing large datasets across diverse platforms.
• The result: CoSAG-nf delivers reproducible, scalable, and comprehensive genome reconstructions with detailed quality reports, enabling advanced microbial genomics research at scale.