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jean — Molecular Biology & Genomics

design_barcodes

Design a set of NGS sample-index barcodes with a guaranteed minimum distance, and report what that set actually corrects — substitutions, or indels too (DNABarcodes).

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.
lengthNobarcode length in bases. In bp.
metricNoerror model. A set correcting one substitution may correct zero indels, so this choice is the design, not a display option. Values: hamming (Hamming (substitutions)), seqlev (Sequence-Levenshtein (indels)), levenshtein (Levenshtein), phaseshift (Phaseshift).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.
filter_gcNokeep only balanced-GC barcodes (suppressed for length ≤ 3). Advanced.
heuristicNoset-construction strategy. Values: conway (Conway (greedy)), clique (Clique), sampling (Sampling), ashlock (Ashlock).conway
min_distanceNorequired minimum distance between any two barcodes — this is what buys the error correction.
filter_tripletsNoreject barcodes containing a homotriplet (AAA…). Advanced.

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
countYeshow many barcodes the search actually found
analysisYesthe set's properties under EVERY metric, not just the design one
barcodesYesthe designed set
warningsYeswhat the search had to say
guaranteeYescorrectable / detectable errors under the design metric

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observed

TDQS

A3.7/5.0
Behavior3/5

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

Annotations declare readOnlyHint=false with destructiveHint=false, which is an unusual profile for a design/compute tool and does not by itself explain behavior. The description adds a genuine behavioral guarantee ('guaranteed minimum distance', reports substitutions vs indels), but says nothing about determinism, cost, or permissions. With sparse annotation coverage this is adequate but not rich.

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?

A single front-loaded sentence with no padding; every clause earns its place, and the dash clause adding the substitution/indel reporting is a meaningful payload rather than filler. Slightly terse, but efficient.

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?

An output schema exists, so the description need not explain return values, and it correctly focuses on what the tool produces. With 8 all-optional parameters and nested _files/_subject, the description could note it runs with sensible defaults, but for a design tool with a documented output schema it is largely complete.

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 every parameter is already documented in the schema, including the metric enum and min_distance. The description echoes the central semantics (min_distance buys error correction, metric determines what is corrected) but adds no format or constraint detail beyond the schema, so the baseline of 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 (Design), resource (NGS sample-index barcodes), and scope (guaranteed minimum distance plus reporting what the set corrects). An agent can distinguish it from siblings like audit_barcodes and export_barcodes, which operate on an existing set rather than creating one.

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

Usage Guidelines3/5

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

The phrase 'NGS sample-index barcodes' implies the context of use, and the '(DNABarcodes)' tag hints at the underlying method, but there is no explicit when-to-use, when-not, or named alternative (e.g., audit_barcodes or design_free_codes). Usage must be inferred.

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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