v0.06 - refactored

• Fixed a bug with the min kmer filter
• Removed some instances where caching temporary files got in the way
• Added a version statement in the usage
• Refactored mashtree_wrapper.pl
• Updated README.md

v0.05 - abundance filter

• Added a new abundance filter that searches for kmer "valleys"
• Enable this filter by specifying --mindepth 0 when using fastq files
• idea from Alex Jironkin and Anthony Underwood, but I created a version that is unfortunately not as fast but does not require any additional dependencies.
  • https://bitsandbugs.org/2016/07/29/mash-and-khmer-abundance/

v0.04

• Sketch size is now an option
• Bootstrapping is done based on input order and neighbor-joining. Thanks to Jo Williams for that idea.
• Slightly better documentation

v0.03

I refactored the code

• bin directory
• wrapper script for running the instances of mashtree.pl in case of bootstrapping
• Mashtree.pm module to help abstract some things

I also validated:

• The tree of 524 genome assemblies from v0.03 looks like the same from an older version

v0.02

• added methods to add assemblies into the mash tree
• Refined raw reads parameters in sketches

Seems to be working with multithreads

v0.01

init