Integrated optimization of experimental and computational workflows improves genome recovery in long-read gut metagenomics

Short-read metagenomic sequencing is widely applied in microbiome research due to its high quality and increasingly more affordable prices. However, it suffers from fragmented reads which limits assembly contiguity and the recovery of complete microbial genomes. In contrast, long-read sequencing, with substantially longer read lengths, can help overcome these limitations. Achieving complete and accurate genome recovery is a central goal in metagenomics. To advance this goal, we present a systematic effort to unify and optimize the long-read sequencing workflow, from experimental sample processing to computational genome assembly, using the CycloneSEQ platform.

Hu, Y., Sun, L., Huang, Y., Jiang, F., Tong, X., Yang, J., Ju, Y., Yang, Z., Liufu, S., Hu, Y., Ma, W., Guo, R., Li, W., Zhang, T., Zhu, X., Zhang, Z.

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