Jean by Melad Labs

fastq_qc

Read-only

FastQC's report on FASTQ reads, every module a default FastQC run reports: per-base quality boxes, per-tile quality (when the headers carry a tile), per-sequence quality, per-base sequence content, per-sequence GC against FastQC's theoretical normal, per-base N content, sequence length distribution, duplication levels, overrepresented sequences with their possible source, and adapter content, each with FastQC's own pass/warn/fail grade and the limit it was graded on.

Input Schema

Name	Required	Description	Default
`reads`	Yes	the reads, as FASTQ: four lines per record, quality line required.
`_files`	No	The 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.
`_subject`	No	The 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.
`adapters`	No	adapters to search for, in FastQC's --adapters format (a name, a tab, a sequence, one per line). Unset searches FastQC's own list. Advanced.
`grouping`	No	how read positions pool into one group: FastQC's default (the first 9 bases one by one, then groups sized to stay under 75), none (one per base, --nogroup) or exponential (--expgroup).	linear
`contaminants`	No	sequences an overrepresented read is matched against for its possible source, in FastQC's --contaminants format (a name, a tab, a sequence, one per line). Unset uses FastQC's own list. Advanced.
`phred_offset`	No	quality encoding: 33 for every modern FASTQ, 64 only for pre-1.8 Illumina (FastQC's --phred64). Advanced.

Output Schema

Name	Required	Description
`failed`	Yes	how many modules FastQC would fail
`grades`	Yes	module name to pass, warn or fail
`report`	Yes	every module's table and grade: perBaseQuality (boxes), perTileQuality (null without tiles), perSequenceQuality, perBaseContent, perSequenceGc (counts, theoretical, mode, stdev, deviationPercent), nContent, lengthDistribution, duplication (percentOfTotal, percentRemaining), overrepresented (sequences with count, percentage, possibleSource), adapterContent
`gcDeviationPercent`	Yes	how far the per-read GC distribution sits from FastQC's normal, as a percent of reads

Schema Changelog

Changes observed during successful MCP inspections.

Changed1 schema field changedOct 25, 2026
- addedOutput schema / properties / gcDeviationPercent / x-unit
```
Added value: +"%"
```
AddedOct 21, 2026

TDQS

B3.2/5.0

Behavior3/5

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

The annotations already establish that this is a read-only, non-destructive, closed-world operation. The description adds useful output-shape behavior by saying all default FastQC modules and pass/warn/fail grades are returned, including per-tile quality only when tile information is present; however, it does not discuss runtime, input handling, or failure modes, and the output schema already carries much of the return structure.

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

Conciseness3/5

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

The purpose is front-loaded, but the description is one very long sentence that exhaustively lists FastQC modules, much of which duplicates information available in the output schema. It is not fluffy, but it is less concise than it could be for an agent that mostly needs to know what the tool does and when to select it.

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?

For a seven-parameter analysis tool with full schema coverage, annotations, and an output schema, the description gives a clear account of what the report contains. Input semantics and safety are covered structurally, and the main missing piece is sibling routing rather than core invocation information.

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 all seven parameters already have documented meaning in the input schema. The description does not add syntax, defaults, or constraints beyond what the schema provides, making the baseline 3 appropriate.

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

Purpose4/5

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

The description clearly identifies a specific analysis, FastQC's report on FASTQ reads, and enumerates the modules it returns. It is more specific than a tautology, but it never names or distinguishes itself from nearby siblings such as read_sequencing_qc, so an agent must infer which QC tool to choose.

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

Usage Guidelines2/5

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

There is no explicit when-to-use or when-not-to-use guidance, no prerequisites, and no named alternative. The QC use case is implied by the title and module list, but the description does not help an agent route between fastq_qc and other read-level or sequencing-QC tools.

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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