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jean — Molecular Biology & Genomics

check_index_pool

Read-only

Will this pool of sample indexes actually sequence? One verdict over the indexes a lab is about to load: duplicates, uniform length, the distance the set really guarantees against the distance it claims, per-cycle color balance on the chosen instrument's own chemistry, the index-2 orientation that instrument reads, and index-hopping exposure — how many i7 x i5 combinations exist against how many are in use, and which swaps would turn one sample's read into another's undetectably. Takes a pasted list or a vendor kit by id. It CHECKS a pool; design_barcodes builds one.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
kitNoa vendor kit id instead of a pasted list — the kit's own indexes are resolved and checked. Ignored when `pool` is given. Values: (No kit — paste a list instead), truseq-single-indexes (TruSeq Single Indexes — Illumina, 24 indexes), truseq-cd-indexes (TruSeq DNA and RNA CD Indexes — Illumina, 96 indexes), idt-truseq-ud-indexes (IDT for Illumina–TruSeq DNA and RNA UD Indexes — Illumina / IDT, 100 indexes), idt-illumina-ud-plate-a (IDT for Illumina UD Indexes, Plate A/Set 1 — Illumina / IDT, 96 indexes), idt-illumina-ud-plate-b (IDT for Illumina UD Indexes, Plate B/Set 2 — Illumina / IDT, 96 indexes), idt-illumina-ud-plate-c (IDT for Illumina UD Indexes, Plate C/Set 3 — Illumina / IDT, 98 indexes), idt-illumina-ud-plate-d (IDT for Illumina UD Indexes, Plate D/Set 4 — Illumina / IDT, 100 indexes). Only applies when pool is not given.
poolNothe pool as text — one row per sample: `name<TAB>i7[<TAB>i5]`, or bare index sequences one per line, with or without a header. Rows that cannot be read are REPORTED with their line number, never dropped.
_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 the distance guarantee is measured under — a pool 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.
i5_cyclesNoindex-2 read length from the run recipe. 0 = use the indexes' own length.
i7_cyclesNoindex-1 read length from the RUN RECIPE, when it differs from the index length — a 10 nt index read at 8 cycles is an 8 nt index for every purpose here. 0 = use the indexes' own length.
instrumentNowhich instrument the run is on. It decides the chemistry the color balance is judged under AND the orientation index 2 is read in — a pool balanced on a NovaSeq 6000 is not balanced on a NovaSeq X.NovaSeq X / X Plus
library_prepNowhich of Illumina's published hopping-rate classes applies. The check multiplies the published RANGE by what this pool can throw away, to report how much is unrecoverable — it never predicts a rate for your run. Values: patterned-examp (Patterned flow cell, ExAmp chemistry), truseq-pcr-free (TruSeq PCR-Free libraries).patterned-examp
required_distanceNothe minimum distance the pool is SUPPOSED to guarantee, if it was designed to one — the check says whether it does. 0 = report the distance without judging it. Advanced.

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
readsYesper index read: cycles, color-balance tier and the per-cycle channel census
checksYesevery check with its own result — a check with no input to run against reports SKIPPED, never passed
hoppingYesindex-hopping exposure: combinations possible against combinations in use, the removable share, and the undetectable swaps
samplesYeshow many samples were checked
skippedYesrows the parse could not read, each with its line number and the reason — these are usually WHY a check refused
verdictYesthe pool-level verdict: `ok`, `warning` or `fail`
failuresYeschecks that FAILED — a warn and a skip are each counted by their own status in `checks`, never folded in here
guaranteeYeshow many errors this pool can CORRECT and DETECT under the chosen metric — the number the whole check exists to establish
closestPairsYesthe pairs that get confused first

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observed

TDQS

A4.2/5.0
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 meaningful behavioral context beyond that: it discloses which properties are evaluated, that hopping exposure is expressed as i7 x i5 combinations in use, and explicitly that it "never predicts a rate for your run" — a useful scope boundary. It does not describe the verdict output shape, but the output schema covers that.

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-loaded with the guiding question ("Will this pool actually sequence?") followed by a dense but purposeful enumeration of the checks, then inputs and a sibling contrast. Every clause earns its place, though the hopping-exposure sentence is long and nested, slightly taxing readability.

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 a zero-required-parameter, read-only analysis tool with an output schema present, the description is complete: it explains what is analyzed, the two input modes, how the error model and instrument shape the verdict, and how it differs from the builder sibling. Return-value detail is rightly left to the output schema.

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 every parameter including the pool-vs-kit mutual exclusivity ("Ignored when pool is given"). The description reinforces that both input paths exist but adds no syntax or format detail beyond what the schema provides, so the baseline of 3 is appropriate.

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) and resource (a pool of sample indexes) and enumerates exactly what verdicts it returns: duplicates, uniform length, distance guarantee vs claim, per-cycle color balance, index-2 orientation, and index-hopping exposure. It explicitly distinguishes itself from the sibling design_barcodes ("It CHECKS a pool; design_barcodes builds one"), so an agent can route correctly without opening either 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?

Names the alternative and the axis that separates them: check vs build, with design_barcodes as the builder counterpart. It also clarifies accepted inputs (a pasted list or a vendor kit by id). There is no explicit when-not or prerequisite guidance, so it falls just short of a full 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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