FastaGuard v0.4.0

FastaGuard v0.4.0

GitHub release artifacts are built from the v0.4.0 tag.

Bioconda and BioContainers publication remain follow-up work after the GitHub
release is available.

Theme: Preflight Readiness + Compare Mode.

This release adds fastaguard compare, readiness categories, index-readiness
checks, submission-readiness advisories, and cohort triage outputs. FastaGuard
remains FASTA preflight QC and does not replace QUAST, BUSCO, BlobToolKit,
CheckM, official submission validators, or annotation workflows.

Highlights

• Adds compare mode for ranking and routing many FASTA files from one command.
• Adds readiness categories so humans and workflow engines can distinguish file,
  structure, alphabet, index, assembly, submission, and machine readiness.
• Adds index-readiness checks for identifier patterns that can break joins,
  indexes, annotations, or downstream sample tracking.
• Adds submission-readiness advisories for FASTA-level issues worth fixing
  before official validators or archive submission.
• Adds cohort JSON, TSV, HTML, and MultiQC-compatible outputs for starter
  multi-sample triage.

Boundary

FastaGuard v0.4.0 stays fast and database-free by default. Compare mode
aggregates FastaGuard's own FASTA-level evidence; it does not infer taxonomy,
prove biological completeness, replace assembly evaluation, or substitute for
official submission validation.

Publication Status

• Source/package metadata is 0.4.0.
• GitHub release binaries are produced from the v0.4.0 tag.
• Published Bioconda and BioContainers packages remain v0.3.0 until packaging
  follow-up is complete.