v1.1.0

• Introduce ability to specify GTDB release and update to using GTDB R220 as default for when users request to auto-download and include all genomes from a particular genus/species.
• Remove need for symlinking genomes locally, instead fastx index files are now written in the same folder as the input genomes and deleted afterwards.
• Parallelization when computing N50 is done by splitting up number of genomes by the number of CPUs allocated and thus writing to at most X number of files at a time, where X is the number of CPUs. This is to address: #4

v1.0.10

• Minor change, added new argument to use https://ftp.ncbi.nlm.nih.gov/genomes instead of https://ftp.ncbi.nih.gov/genomes in case there are issues with connecting to the latter. This gets passed to ncbi-genome-download's -u argument.

Full Changelog: v1.0.9...v1.0.10

v1.0.9

• Support for gzipped files added (#4)
• GTDB/NCBI downloaded genomes are now kept in gzip form
• FASTA files ending in *.fas now allowed (#4)
• If local input genomes are provided, default behavior is now to symlink files in the skDER results directory and do indexing for N50 calculation there.
• FASTA confirmation now optional (might paralelize in the future and turn back on as default - but currently iterative) - it can take a while if there are a lot of files.

Full Changelog: v1.0.8...v1.0.9

v1.0.8

• Fix broken GTDB-based downloading feature.
• Polish names for genomic assemblies downloaded based on GTDB species names.

Full Changelog: v1.0.7...v1.0.8

v1.0.7

• Corrected faulty usage of the -s option in skani triangle and now set it to the default value. This should now result in the more accurate ANI estimates being used for the dereplication methods as intended.
• Updated stats and runtime info for running dynamic/greedy approaches on the Wiki.
• Added new secondary clustering option, -n which will report the relation/distance of all genomes in the input set to their nearest representative genome.

Full Changelog: v1.0.6...v1.0.7

v1.0.6

• Mostly just updates to the README & help function.
• Added missing library import statements in util.py

Full Changelog: v1.0.5...v1.0.6

v1.0.5

• update packaging of program + installation guide

v1.0.4

• fix SKDER_PATH now that skder moved to bin/

v1.0.2

updates for v.1.0.2

• KEY: Correct overflow issue in C++ code related to integer multiplication in computing scores for dynamic dereplication approach
• Introduce a greedy set cover dereplication approach as an alternate method
• Improve code + documentation organization
• Add test case

Full Changelog: v1.0.1...v1.0.2

v1.0.1

• Create directory with representative genomes in the output directory.
• Add version flag , change input for --genomes argument from accepting a directory to multiple paths to genome files.
• Update Enterococcus dereplication showcasing.

Full Changelog: v1.0...v1.0.1