Sequence file inventory enumeration

Skill HolobiomicsLab/asb-skill-collections/collections/metabolomics/v2/skills/sequence-file-inventory-enumeration

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Install

npx -y skills add HolobiomicsLab/asb-skill-collections --skill sequence-file-inventory-enumeration

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Use when when you maintain a repository with local sequence files and need to determine which sequences are not publicly available in NCBI GenBank/RefSeq databases—for example, to distinguish proprietary or supplementary sequence data from publicly registered entries, or to create an inventory.

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SKILL.md

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sequence-file-inventory-enumeration

License: restricted — no clear open-source license detected for the underlying tool; verify licensing before commercial use or redistribution.

Summary

Systematically enumerate and cross-reference sequence files in a local repository (MIBiG's genbanks directory) against NCBI GenBank/RefSeq to identify sequences that are unavailable in public databases. This skill is essential for curating and documenting unique or restricted sequence assets.

When to use

When you maintain a repository with local sequence files and need to determine which sequences are not publicly available in NCBI GenBank/RefSeq databases—for example, to distinguish proprietary or supplementary sequence data from publicly registered entries, or to create an inventory manifest for data governance.

When NOT to use

Input directory contains only already-validated NCBI accessions with no local sequences—use a simple accession lookup instead.
Sequences are known to be private or restricted by license and you do not need public availability confirmation—enumeration is unnecessary overhead.

Inputs

Local sequence file directory (e.g., genbanks directory in MIBiG repository)
Sequence file metadata (filename, entry identifier, optional NCBI accession)
NCBI GenBank/RefSeq database (via E-utilities or BLAST index)

Outputs

Structured inventory manifest (CSV or JSON format)
Manifest columns: file path, sequence identifier, GenBank accession, availability status (local-only or public)

How to apply

Clone or access the target repository (e.g., MIBiG's github.com/mibig-secmet/mibig-json) and list all sequence files in the designated directory (e.g., genbanks). For each file, extract its entry identifier and any embedded NCBI accession number. Use NCBI E-utilities or local BLAST to query whether that accession exists in GenBank/RefSeq; if no accession is present or the query returns no hit, flag it as local-only. Compile results into a structured manifest (CSV or JSON) with columns for file path, sequence identifier, GenBank accession (if present), and availability status (local-only or public). The rationale is to create a transparent, machine-readable record of which sequences are unique to the repository versus mirrored from public sources.

Related tools

NCBI E-utilities (Query NCBI GenBank/RefSeq accession identifiers to determine if a sequence is publicly registered)
BLAST (Local or remote sequence similarity search to cross-reference local sequences against GenBank/RefSeq and confirm accession status)

Evaluation signals

Manifest file exists and contains all expected columns (file path, sequence identifier, GenBank accession, availability status).
No sequence files from the input directory are missing from the manifest; row count equals file count.
For each row marked 'public', the GenBank accession field is non-empty and validated; for 'local-only' rows, accession is empty or null.
Spot-check: manually verify 3–5 flagged 'local-only' sequences by querying NCBI directly; no false negatives (sequences marked local but actually public in GenBank).
Manifest is well-formed JSON or valid CSV with no malformed cells or unexpected null values.

Limitations

NCBI E-utilities queries may have rate limits or temporary unavailability; plan for retry logic or fallback to manual spot-checks.
Sequences without embedded NCBI accessions cannot be definitively cross-referenced unless you perform full BLAST alignment, which is slower and may not always yield a clear match.
The MIBiG repository maintains only 'a handful' of local sequences, so the inventory may be small and may not justify high automation investment.
Accession identifiers may be outdated or withdrawn from NCBI; the manifest reflects status at query time only.

Evidence

[readme] The genbanks directory contains a handful of sequence files that are not available from NCBI's GenBank/RefSeq databases: "The genbanks directory contains a handful of sequence files that are not available from NCBI's GenBank/RefSeq databases."
[other] Scan the genbanks directory, cross-reference against NCBI accession identifiers, and compile results into a structured manifest: "Scan the genbanks directory to list all sequence files and their metadata. 3. Cross-reference each file against NCBI GenBank/RefSeq accession identifiers (using NCBI E-utilities or local BLAST) to"
[other] Output should be CSV or JSON with columns for file path, sequence identifier, GenBank accession, and availability: "Output the manifest as a CSV or JSON file with columns for file path, sequence identifier, GenBank accession, and availability (local-only or public)."
[other] Tools to use for cross-referencing and validation: "tools: NCBI E-utilities, BLAST"