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

Long-read gut metagenomics on the CycloneSEQ platform shows improved genome recovery when upstream magnetic-plate DNA extraction with pretreatment is used, linked to broader microbial recovery.

• Why it matters: Short-read fragmentation limits assembly contiguity and complete genome recovery, so optimizing long-read workflows is needed to improve accuracy and completeness in fecal metagenomic studies.
• What they did: The study systematically optimized experimental and computational steps on CycloneSEQ, then benchmarked assemblies by integrating matched CycloneSEQ long-read data with DNBSEQ short-read data.
• The result: In a fecal metagenomic dataset, long-read-first assembly followed by short-read polishing achieved strong overall performance across recovery, contiguity, and sequence accuracy, with results remaining dependent on the evaluation metric.

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