singlem
Taxonomic profiling of microbial and phage metagenomes
All Skills in This Repository (1)
Pure Emerald Level IndicatorsFrequently Asked Questions
FAQPage SchemaHow to install SingleM?▼
Run `npx skills add wwood/singlem --all -g -y` in your terminal to install all skills in this suite globally.
What does SingleM do?▼
SingleM profiles shotgun metagenomes by targeting single-copy marker genes, producing GTDB-based taxonomic profiles that estimate the relative abundance of bacteria, archaea, and phages in a sample.
Can SingleM handle long-read sequencing data?▼
Yes. SingleM supports Nanopore R10.4.1+ and PacBio HiFi long reads using the same pipe command, and it auto-detects read length.
How do I profile phages in metagenomic data?▼
Use the bundled Lyrebird command, which works like singlem pipe but profiles dsDNA phages using over 500 marker genes and vConTACT3-based taxonomy.
Can I update results without rerunning the full pipeline?▼
Yes. Save an archive OTU table during the initial run, then use singlem renew to re-assign taxonomy against a newer reference metapackage without reprocessing the reads.
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