v1.3.4

• Fix skder low_mem_greedy mode's usage of skani sketch to account for updates made in skani v0.3.0.

Full Changelog: v1.3.3...v1.3.4

v1.3.3

• Introduce new 'low_mem_greedy' dereplication mode in skder to efficiently handle really large datasets.
• Fix issues with automated downloading of genomes from NCBI due to updating listings and add catch for bad files.
• Switch cidder's skani-based secondary clustering from using skani triangle to skani dist.

Full Changelog: v1.3.2...v1.3.3

v1.3.2

• Fix: Correct default value of --skani-triangle-parameters skDER which was outdated. This parameter was recently updated to request a screening parameter of X%, where X = ANI threshold - 10%, by default. It was however being set as -s 90.0 by default my mistake (the previous default) - this is now corrected.

What's Changed

• Update to v1.3.2 by @raufs in #10

New Contributors

• @raufs made their first contribution in #10

Full Changelog: v1.3.1...v1.3.2

v1.3.1

Minor fix: Update argument descriptions for inputs to clarify that genome/proteome files input for CiDDER need to be uncompressed unlike for skDER where gzipped files are allowed. Also added a check for this in case users provide compressed inputs.

Full Changelog: v1.3.0...v1.3.1

v1.3.0

• Restructure code and introduce new modules to simplify the main programs of skder and cidder.
• Incorporate faster way to download genomes from NCBI belonging to a single genus/species of interest in GTDB.
• Incorporate the latest GTDB release R226.
• Add new option to cidder to select additional representative genomes if X% of non-representative genomes are not contained by an individual representative genome. This is performed as a secondary step after the primary representative selection method.
• Change the default ANI cutoff from 99.0% to 99.5% identity in skder to reflect thresholds coinciding with sequence type designations as reported by Rodriguez-R et al. 2023.
• Lowered the default AF* threshold from 90% to 50% to reflect perspective/insight shared in the dRep documentation.
• Allow proteomes to be provided as inputs for CiDDER.

* = initially wrote ANI by mistake.

Full Changelog: v1.2.9...v1.3.0

v1.2.9

Minor updates

• make overwriting the output directory more safe and introduce user prompt.
• strip away quotes in string arguments with spaces in case they are not processed properly. (related to #8).

Full Changelog: v1.2.8...v1.2.9

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