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jean — Molecular Biology & Genomics

audit_barcodes

Read-only

Check an index set you ALREADY have, rather than designing a new one: the minimum distance between any two, how many errors that guarantees correcting, the full distance matrices, and — optionally — the subset that survives pruning to a stricter error budget. This is the question asked of a set inherited from a kit or a previous experiment.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
_filesNoThe project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
metricNoerror model to audit against — a set safe under substitutions may be unsafe under indels. Values: hamming (Hamming (substitutions)), seqlev (Sequence-Levenshtein (indels)), levenshtein (Levenshtein).seqlev
_subjectNoThe record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.
barcodesYesthe index sequences to audit.
prune_to_errorsNoalso report the subset that would survive pruning to a free code correcting this many errors. 0 = do not prune. Advanced.
required_distanceNothe minimum distance the set is supposed to have — the audit says whether it does.

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
keptYesthe barcodes surviving `prune_to_errors` (the whole set when pruning is off)
auditYesthe verdict: the set's real minimum distance, what it guarantees, and every pair that falls short
droppedYeshow many the prune removed
analysisYesper-metric analysis of the whole set
matricesYesthe pairwise distance matrix under each metric
distanceMapYesthe pairwise distance matrix under the chosen metric, as a heatmap

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observed

TDQS

A4.1/5.0
Behavior4/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

Annotations already declare readOnlyHint=true, destructiveHint=false, openWorldHint=false, so the safety profile is covered. The description adds valuable behavioral content beyond that: it discloses the concrete outputs (minimum distance, error-correction guarantee, distance matrices, optional pruned subset), which is what the agent needs to know about the result.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness4/5

Is the description appropriately sized, front-loaded, and free of redundancy?

Front-loads the key distinction (audit existing vs design new) before enumerating outputs. The em-dash chain is slightly dense and the closing sentence is somewhat decorative, but no sentence is wasted.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness4/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

With an output schema present, return values needn't be spelled out, and annotations carry the safety profile. The description covers purpose, alternative, and the audit computations; it is complete enough for correct selection and invocation.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters3/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema description coverage is 100%, so the schema already documents metric, prune_to_errors, required_distance and the record params. The description gestures at pruning ('subset that survives pruning to a stricter error budget') but adds no syntax or format detail beyond the schema, so baseline 3 applies.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose5/5

Does the description clearly state what the tool does and how it differs from similar tools?

States a specific verb (check/audit) and resource (an index set you already have), and explicitly separates itself from the design-a-new-one path. An agent can distinguish this from design_barcodes/design_free_codes without opening the schema.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines4/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

Explicitly frames the use case: 'Check an index set you ALREADY have, rather than designing a new one,' and gives the scenario ('inherited from a kit or a previous experiment'). It names the alternative category rather than a specific sibling tool, so a 4 rather than 5.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

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