Cleans a shotgun metagenome of everything that is not the target community before profiling - host-read depletion (Hostile, bowtie2/T2T-CHM13), reagent/kitome contamination control with blanks and decontam, mock-community validation, and depth-adequacy checks (Nonpareil). Covers why a metagenomic result is a position in a choice-chain rather than a direct observation, why extraction is the experiment, why a low-biomass community can be entirely kitome, why absence means not-detectable-by-this-chain, and why a confident classifier call can still be wrong when the reference is contaminated. Use when designing controls, removing host reads, identifying reagent contaminants, validating with mocks, or judging whether a low-biomass result is real. For adapter/quality trimming see read-qc; for MAG-level decontamination see genome-assembly/metagenome-assembly.
Install with
Claude CodeCodexCursorGitHub CopilotGemini CLI
Supported by the Atlas install prompt. Skill-specific requirements vary.
Skill stats
Skills1CategoryScience & researchStars0
About this skill
Cleans a shotgun metagenome of everything that is not the target community before profiling - host-read depletion (Hostile, bowtie2/T2T-CHM13), reagent/kitome contamination control with blanks and decontam, mock-community validation, and depth-adequacy checks (Nonpareil). Covers why a metagenomic result is a position in a choice-chain rather than a direct observation, why extraction is the experiment, why a low-biomass community can be entirely kitome, why absence means not-detectable-by-this-chain, and why a confident classifier call can still be wrong when the reference is contaminated. Use when designing controls, removing host reads, identifying reagent contaminants, validating with mocks, or judging whether a low-biomass result is real. For adapter/quality trimming see read-qc; for MAG-level decontamination see genome-assembly/metagenome-assembly.
Quick start
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Cleans a shotgun metagenome of everything that is not the target community before profiling - host-read depletion (Hostile, bowtie2/T2T-CHM13), reagent/kitome contamination control with blanks and decontam, mock-community validation, and depth-adequacy checks (Nonpareil). Covers why a metagenomic result is a position in a choice-chain rather than a direct observation, why extraction is the experiment, why a low-biomass community can be entirely kitome, why absence means not-detectable-by-this-chain, and why a confident classifier call can still be wrong when the reference is contaminated. Use when designing controls, removing host reads, identifying reagent contaminants, validating with mocks, or judging whether a low-biomass result is real. For adapter/quality trimming see read-qc; for MAG-level decontamination see genome-assembly/metagenome-assembly.
About this listing
Category
Science & research
Reported license
Not specified
Listing language (estimated)
English
Review status
Not individually reviewed
Agent compatibility
Atlas installation supports Claude Code, Codex, and Cursor. Skill-specific dependencies and features are checked during setup.
Claude Code
Codex
Cursor
GitHub Copilot
Gemini CLI