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cblaster and clinker

Status: available upstream; public end-to-end wrapper fixture planned.

cblaster searches for co-located homologs by remote NCBI search or local DIAMOND search. clinker compares GenBank cluster records and produces an interactive HTML plot.

Current public releases reviewed on 2026-08-30 are cblaster 1.4.2 and clinker 0.0.32.

Install

python3 -m pip install "cblaster>=1.4.0" "clinker>=0.0.32"
cblaster --version
clinker --version

These are minimum versions, not exact pins.

Minimal pattern

cblaster search \
  --query_file <QUERY_FASTA> \
  --mode remote \
  --output <OUTPUT_DIR>/clusters.csv \
  --plot <OUTPUT_DIR>/clusters.html

clinker <CLUSTER_GENBANK_FILES> --plot <OUTPUT_DIR>/clinker.html

The current clinker CLI does not document --output_html or --output_svg. Export a static image through a separately documented browser or rendering step when needed.

Output contract

Keep the query ledger, search mode, database and access date, cblaster and clinker versions, GenBank inputs, tabular results, HTML plot, and hashes. Local search requires prepared genome records; remote search depends on the current upstream service and database behavior.

Sources: cblaster documentation, cblaster on PyPI, and clinker.