Changelogs » Singlem

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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