Assembly Dereplicator v0.3.2

This release adds a new dereplication target: --fraction. Thanks to @mbhall88 for the idea and his help coding it!

Assembly Dereplicator v0.3.1

This version fixes a bug: mash sketch could result in an 'Argument list too long' error if there were a lot (tens of thousands) of input genomes. Assembly Dereplicator now runs mash sketch with a FOFN input to avoid this problem.

Also, the minimum required version of Python increased from 3.6 to 3.8.

Assembly Dereplicator v0.3.0

This version changes the dereplication algorithm. Instead of a using single-linkage clustering, it now progressively removes one assembly from the closest pair until the target dereplication is complete. This allows for dereplication to either a distance threshold or a defined number of genomes. See the README for more info.

If you'd like to use the old single-linkage clustering approach, that's in the last release: v0.1.1.

Assembly Dereplicator v0.1.1

This release contains two small changes:

• The addition of a --verbose option
• A high default value for --batch_size to effectively turn off batching by default

Assembly Dereplicator v0.1.0

First release!