Manifest Generation And Documentation

Reconstruct the non-NCBI sequence inventory from the genbanks directory

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

Summary

Generate a structured inventory manifest of sequence files held in a repository's local genbanks directory that are not available from NCBI's GenBank/RefSeq databases. This skill reconciles local file metadata with public sequence databases to identify and document sequences unique to the repository.

When to use

Apply this skill when you need to audit a bioinformatics repository (such as MIBiG) to determine which sequence files are maintained locally but lack public accessions in NCBI GenBank/RefSeq. Use this to support curation workflows, data provenance tracking, or to identify candidate sequences for public release.

When NOT to use

• Input sequence files are already linked to public NCBI accessions and no audit of local-only sequences is needed.
• The genbanks directory does not exist or is empty in the target repository.
• NCBI E-utilities or BLAST access is unavailable and cross-referencing cannot be performed.

Inputs

• MIBiG repository cloned from github.com/mibig-secmet/mibig-json
• genbanks directory containing sequence files
• NCBI GenBank/RefSeq database (via E-utilities or BLAST)

Outputs

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

How to apply

Clone or access the target repository and enumerate all files in the genbanks directory, extracting sequence identifiers and any embedded NCBI accession numbers. For each file, cross-reference the accession against NCBI GenBank/RefSeq using NCBI E-utilities or local BLAST searches to establish availability status. Files with valid public accessions are marked as publicly available; files with no matching accession or accession lookup failures are flagged as local-only. Compile the results into a structured manifest (CSV or JSON) recording filename, entry identifier, accession (if present), and a local-only status flag. This reconciliation approach ensures completeness and helps distinguish curated or proprietary sequences from those already in the public domain.

Related tools

• NCBI E-utilities (Query NCBI GenBank/RefSeq databases to verify accession availability and retrieve sequence metadata for cross-referencing)
• BLAST (Perform local sequence similarity searches to determine whether sequences are present in NCBI GenBank/RefSeq or are unique to the local genbanks directory)

Evaluation signals

• Manifest file is generated and contains all expected columns: file path, sequence identifier, GenBank accession, and availability flag.
• All files in the genbanks directory are represented in the manifest with no missing entries.
• Accession lookups return consistent results when spot-checked against NCBI's online interfaces or local BLAST databases.
• Local-only sequences have blank or 'N/A' accession fields, while public sequences carry valid NCBI accessions and availability = 'public'.
• Manifest can be parsed as valid CSV/JSON and round-trips without data loss.

Limitations

• Some sequence files in the genbanks directory may lack embedded accession identifiers, requiring sequence-level similarity searches (BLAST) which may be computationally expensive or ambiguous for highly similar or fragmented sequences.
• NCBI E-utilities queries may timeout or rate-limit if the number of accessions is very large; batch queries or delays may be necessary.
• Sequences that are novel or significantly divergent from public databases may not be detected as local-only without full de novo assembly or annotation.
• No changelog is available in the repository documentation to track historical changes to the genbanks directory, limiting provenance tracking.

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] Cross-reference each file against NCBI GenBank/RefSeq accession identifiers (using NCBI E-utilities or local BLAST) to determine availability status.: "Cross-reference each file against NCBI GenBank/RefSeq accession identifiers (using NCBI E-utilities or local BLAST) to determine availability status"
• [other] Compile results into a structured manifest recording filename, entry identifier, accession (if present), and local-only status flag.: "Compile results into a structured manifest recording filename, entry identifier, accession (if present), and local-only status flag"
• [other] Output the manifest as a CSV or JSON file with columns for file path, sequence identifier, GenBank accession, and availability (local-only or public).: "Output the manifest as a CSV or JSON file with columns for file path, sequence identifier, GenBank accession, and availability (local-only or public)"