v1.2.8

• Minor changes: update granet help function & graph creation to have representatives listed last and thus their nodes be shown on top and not hidden underneath non-representative genomes in really large graphs.

v1.2.7

• Update granet to make it deterministic and also introduce the --random-seed option to allow changing the layout if desired.
• Fix indentation issues in help function and slight updates to logging and messages in CiDDER and skDER.
• Create CiDDER_Results.txt file in CiDDER to capture the order in which representative genomes are selected.

Full Changelog: v1.2.6...v1.2.7

v1.2.6

• Make "greedy" mode the default algorithm in skder
• Correct stumbling on gzipped files with new method to calculate N50s introduced in v1.2.4.
• Introduce granet - for creating network visuals of genomes and where representative genomes selected fall.
• Update help functions of skder and cidder to include citation notice for skani and CD-HIT, respectively.

What's Changed

• Updated Docker folder by @Lolli-AK in #7

Full Changelog: v1.2.5...v1.2.6

v1.2.5

• In skDER, set the default value of -p - controlling additional arguments to pass to skani triangle - from nothing ( ) to -s 90.0 to increase the screening parameter's value to 90.0 from the default value of 80.0.
• Add support for providing directory paths, as well as files, to the -g/--genomes argument where the directories contain genome files to (also) include in skder/cidder analyses.
• Begin development of Docker-based installation support - including convenience bash wrapper (still progress).

What's Changed

• Docker files by @Lolli-AK in #6

New Contributors

• @Lolli-AK made their first contribution in #6

Full Changelog: v1.2.4...v1.2.5

v1.2.4

• Introduce mgecut - a program that can use PhiSpy or geNomad to predict MGEs in genomes and filter them out prior to genomic dereplication.
• Integrate mgecut usage into skder and cidder .
• Switch to simple python implementation of N50 adapted from: https://gist.github.com/dinovski/2bcdcc770d5388c6fcc8a656e5dbe53c instead of using pyfastx.

Full Changelog: v1.2.3...v1.2.4

v1.2.3

• update and further polish arguments (e.g. underscores to dashs).
• add options for secondary clustering for cidder using protein cluster containment* and/or skani (#5).

Full Changelog: v1.2.2...v1.2.3

v1.2.2

• Add memory option for CD-HIT usage in cidder and set default to unlimited.
• Cosmetic changes to code / comments / help-function

Full Changelog: v1.2.1...v1.2.2

v1.2.1

• Correct for default parameter settings in CiDDER
• Add/update expected test results
  

v1.2.0

• Introduce CiDDER - a CD-HIT based dereplication program to ensure you properly sample the pangenome space of a species/genus.
• Introduce new option to skDER to test a bunch of cutoffs for ANI and AF and generate a heatmap on the number of representative genomes that results from different combinations. E.g. useful if you want to limit your analysis to X genomes but don't know what ANI/AF cutoffs to use.

Full Changelog: v1.1.1...v1.2.0

v1.1.1

• add creation of "COMPLETED.txt" at the very end of skDER for incorporation in workflows.
• add option to build indices locally when computing N50s instead of in the directory of the input genome