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SingleM Taxonomic Profiling Skill

Generate GTDB-based taxonomic profiles from metagenomic samples using SingleM marker windows.

194|24|Updated May 28, 2015
Search Tags:#pipeline#taxonomy#profiles#metagenomics#gtdb#singlem
One-click install
npx skills add https://github.com/wwood/singlem --skill singlem-taxonomic-profiling-skill
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: SingleM Taxonomic Profiling Skill
Source: https://github.com/wwood/singlem/tree/main/docs
Command: npx skills add https://github.com/wwood/singlem --skill singlem-taxonomic-profiling-skill

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

Metagenomic samples often require fast, scalable taxonomic profiling to understand community composition; SingleM provides GTDB-based taxonomic profiles from marker-windows.

Core Features & Use Cases

  • GTDB-based taxonomic profiling: Profiles are generated from 20 amino-acid windows within single-copy marker genes to assign taxonomy.
  • Long- and short-read support: Works with both short- and long-read data, and can handle novel lineages.
  • End-to-end workflow: Generates OTU tables and condensed taxonomic profiles via the pipe workflow; supports downloading reference metapackage data.

Quick Start

Run singlem pipe with your reads to produce a GTDB-based taxonomic profile.

Frequently Asked Questions about SingleM Taxonomic Profiling Skill

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I profile shotgun metagenomes to get GTDB taxonomies?▼

The singlem pipe workflow generates both OTU tables and condensed taxonomic profiles end-to-end, using SingleM's 20 amino acid windows within single-copy marker genes to extract and assign GTDB taxonomy from your reads.

What is GTDB-based taxonomic profiling from marker-windows?▼

GTDB-based taxonomic profiling uses 20 amino acid windows within single-copy marker genes to assign taxonomy, enabling fast and scalable analysis of metagenomic community composition while supporting the detection of novel lineages.

Can I use metagenomic profiling for both short-read and long-read data?▼

Yes, metagenomic profiling with SingleM supports both short-read and long-read data. It also handles novel lineages, ensuring accurate taxonomic assignment across different sequencing technologies.

Do I need conda or Docker to run metagenomic taxonomic profiling?▼

Yes, you need a conda or Docker environment setup to run the workflow. You also need to download the reference metapackage data using the singlem data command before profiling your samples.

What outputs do I get from metagenomic taxonomic profiling?▼

The end-to-end pipe workflow outputs OTU tables and condensed taxonomic profiles, providing a comprehensive view of the microbial community composition derived from your metagenomic reads.

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