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* Appraise can now generate 'appraisal plots' * Use of smafa / SQLite rather than BLAST+ / VSEARCH for 'query' and clustering. SingleM databases (.sdb) will need to be regenerated. * SingleM databases can now be queried via taxonomy or sample name * Overhaul of command line help messages * Appraise can now appraise assemblies as well as genomes * Various bug fixes and enhancements
* Fix for installation through PyPI.
* Fix bug in singlem query where some results were omitted. * Detect when max_target_seqs has been reached in singlem query.
* Overhauled makedb/query. Database creation is now faster and querying more accurate, especially for OTUs with gaps. Old databases should be re-generated. * summarise: Added BIOM and wide format outputs - props to Steve Robbins and Louis Monaghan for the suggestions. * appraise: Default to genus-level similarity cutoff.
* Now installable via pip / PyPI.
* Speed improvements for singlem query * Memory improvements for singlem makedb * db: Use and require the new diamond version / database format * summarise: Only output to a single html for --krona where possible