Jean by Melad Labs

align_read

Read-only

Pairwise-align ONE sequencing read against a reference and hand on the two gapped rows, so the read can be graded. Needleman-Wunsch with free end gaps and the IUPAC substitution matrix — SeqTrace's aligner, the same call the trace editor makes, so a pipeline and the panel align a read identically. Leave reference unset to align against the record this step runs on.

Input Schema

Name	Required	Description
`read`	Yes	the read's bases — wire a trace reader's `sequence` output here, or paste them.
`_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.
`reference`	No	what to align against. Unset, it is the record this step runs on (the open plasmid, or an upstream product wired into the subject).

Output Schema

Name	Required	Description
`columns`	Yes	the alignment's width, gaps included
`identity`	Yes	% identity over the columns where both rows have a base (gaps excluded)
`mismatches`	Yes	columns where the two rows carry different bases
`alignedRead`	Yes	the read with gaps inserted — wire into `verify_read.aligned_read`
`referenceLength`	Yes	the reference's ungapped length in bp — wire into `verify_read.target_len`
`alignedReference`	Yes	the reference with gaps inserted — wire into `verify_read.aligned_ref`

Schema Changelog

Changes observed during successful MCP inspections.

Changed2 schema fields changedOct 25, 2026
- addedOutput schema / properties / identity / x-unit
```
Added value: +"%"
```
- addedOutput schema / properties / referenceLength / x-unit
```
Added value: +"bp"
```
First observedOct 20, 2026

TDQS

A4.3/5.0

Behavior5/5

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

Annotations already establish that this is a safe, non-destructive, closed-world read operation. The description adds substantial unannotated behavior: Needleman-Wunsch with free end gaps, the IUPAC substitution matrix, SeqTrace parity, and deterministic alignment identical to the trace editor.

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

Conciseness5/5

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

The key action and output are front-loaded in the first sentence. The remaining sentences add useful algorithm and default-reference context without padding.

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

Completeness5/5

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

For an alignment tool with a fully described schema and an output schema, the description covers purpose, algorithm, determinism, and the important `reference` default. No essential invocation detail appears to be missing.

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 `read`, `reference`, `_files`, and `_subject`. The description's note about leaving `reference` unset largely repeats the schema's own explanation, adding no new syntax, constraints, or examples beyond the structured fields.

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?

The description gives a specific verb and resource: pairwise-align ONE sequencing read against a reference, producing two gapped rows. The emphasis on ONE read and pairwise alignment distinguishes it from broader siblings such as align_sequences or compare_reads_to_reference.

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?

It implies the use case is grading a read against a reference and explains the default behavior when `reference` is unset. However, it does not explicitly name when to choose this over siblings like align_sequences, compare_reads_to_reference, or verify_read, nor does it state exclusions.

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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