doc: update changelog

docs/usage/changelog.md

@@ -3,6 +3,105 @@
 
 # Change log
 
+## 2.17
+
+### Skani
+The tool Skani claims to be better and faster than the combination of mash + FastANI as used by dRep
+I implemented the skin for species clustering. 
+We now do the species clustering in the `atlas run binning` step. 
+So you get information about the number of dereplicated species in the binning report. This allows you to run different binners before choosing the one to use for the genome annotation. 
+Also, the file storage was improved all important files are in `Binning/{binner}/`
+
+
+
+My custom species clustering does the following steps:
+
+1. Pre-cluster genomes with *single-linkage* at 92.5 ANI. 
+2. **Re-calibrate checkm2 results.**
+ - If a minority of genomes from a pre-cluster use a different translation table they are removed
+ - If some genomes of a pre-cluster don't use the specialed completeness model we re-calibrate completeness to the minimum value.
+ This ensures that not a bad genome evaluated on the general model is preferred over a better genome evaluated on the specific model.
+See also https://silask.github.io/post/better_genomes/ Section 2.
+- Drop genomes that don't correspond to the filter criteria after re-calibration
+3. Cluster genomes with ANI threshold default 95%
+4. Select the best genome as representative based on the Quality score Completeness - 5x Contamination
+
+
+
+
+
+### New Contributors
+* @jotech made their first contribution in https://github.com/metagenome-atlas/atlas/pull/667
+
+## 2.16
+
+ * gtdb08
+
+## 2.15
+
+* Use Gunc
+* New Folder organisation: Main output files for Binning are in the new folder `Binning`
+* Use hdf-format for gene catalogs. Allow efficient storage and selective access to large count and coverage matrices from the genecatalog. (See docs for how to load them) https://github.com/metagenome-atlas/atlas/pull/621
+* Semibin v. 1.5 by @SilasK in https://github.com/metagenome-atlas/atlas/pull/622
+
+
+## 2.14
+
+* Support for checkm2  by @SilasK in https://github.com/metagenome-atlas/atlas/pull/607
+
+Thank you @trickovicmatija for your help.
+
+**Full Changelog**: https://github.com/metagenome-atlas/atlas/compare/v2.13.1...v2.14.0
+## 2.13
+
+* use minimap for contigs, genecatalog and genomes in https://github.com/metagenome-atlas/atlas/pull/569  https://github.com/metagenome-atlas/atlas/pull/577
+* filter genomes my self  in https://github.com/metagenome-atlas/atlas/pull/568
+The filter function is defined in the config file:
+```
+genome_filter_criteria: "(Completeness-5*Contamination >50 ) & (Length_scaffolds >=50000) & (Ambigious_bases <1e6) & (N50 > 5*1e3) & (N_scaffolds < 1e3)"
+```
+The genome filtering is similar as other publications in the field, e.g. GTDB. What is maybe a bit different is that genomes with completeness around 50% **and** contamination around 10% are excluded where as using the default parameters dRep would include those. 
+
+* use Drep again  in https://github.com/metagenome-atlas/atlas/pull/579
+We saw better performances using drep. This scales also now to ~1K samples
+* Use new Dram version 1.4 by in https://github.com/metagenome-atlas/atlas/pull/564
+
+
+**Full Changelog**: https://github.com/metagenome-atlas/atlas/compare/v2.12.0...v2.13.0
+
+## 2.12
+
+* GTDB-tk requires rule `extract_gtdb` to run first by @Waschina in https://github.com/metagenome-atlas/atlas/pull/551
+* use Galah instead of Drep 
+* use bbsplit for mapping to genomes (maybe move to minimap in future)
+* faster gene catalogs quantification using minimap. 
+* Compatible with snakemake v7.15
+### New Contributors
+* @Waschina made their first contribution in https://github.com/metagenome-atlas/atlas/pull/551
+
+**Full Changelog**: https://github.com/metagenome-atlas/atlas/compare/v2.11.1...v2.12.0
+
+## 2.11
+* Make atlas handle large gene catalogs using parquet and pyfastx (Fix #515)
+
+parquet files can be opened in python with 
+```
+import pandas as pd
+coverage = pd.read_parquet("working_dir/Genecatalog/counts/median_coverage.parquet")
+coverage.set_index("GeneNr", inplace=True)
+
+```
+
+and in R it should be something like:
+
+```
+arrow::read_parquet("working_dir/Genecatalog/counts/median_coverage.parquet")
+
+```
+
+
+**Full Changelog**: https://github.com/metagenome-atlas/atlas/compare/v2.10.0...v2.11.0
+
 ## [2.10](https://github.com/metagenome-atlas/atlas/compare/v2.9.1...v2.10.0) 
 
 ### Features
@@ -21,3 +120,48 @@
 * @alienzj made their first contribution to fix config when run DRAM annotate in https://github.com/metagenome-atlas/atlas/pull/495
 
 
+## 2.8
+This is a major update of metagenome-atlas. It was developed for the [3-day course in Finnland](https://silask.github.io/talk/3-day-course-on-metagenome-atlas/), that's also why it has a finish release name. 
+
+
+### New binners
+It integrates bleeding-edge binners `Vamb` and `SemiBin` that use Co-binning based on co-abundance. Thank you @yanhui09 and @psj1997 for helping with this. The first results show better results using these binners over the default. 
+
+[See more](https://metagenome-atlas.readthedocs.io/en/v2.8.0/usage/output.html#binning)
+
+### Pathway annotations
+The command `atlas run genomes` produces genome-level functional annotation and Kegg pathways respective modules. It uses DRAM  from @shafferm with a hack to produce all available Kegg modules. 
+
+[See more](https://metagenome-atlas.readthedocs.io/en/v2.8.0/usage/output.html#annotations)
+
+### Genecatalog
+The command `atlas run genecatalog` now produces directly the abundance of the different genes. See more in #276 
+
+> In future this part of the pipeline will include protein assembly to better tackle complicated metagenomes. 
+
+### Minor updates
+
+#### Reports are back
+See for example the [QC report](https://metagenome-atlas.readthedocs.io/en/v2.8.0/_static/QC_report.html)
+
+#### Update of all underlying tools
+All tools use in atlas are now up to date.  From assebler to GTDB.
+The one exception is, BBmap which contains a [bug](https://sourceforge.net/p/bbmap/tickets/48/) and ignores the minidenty parameter.
+
+#### Atlas init 
+Atlas init correctly parses fastq files even if they are in subfolders and if paired-ends are named simply  Sample_1/Sample_2. @Sofie8 will be happy about this.
+Atlas log uses nice colors.
+
+#### Default clustering of Subspecies
+
+The default ANI threshold for genome-dereplication was set to 97.5% to include more sub-species diversity. 
+
+[See more](https://metagenome-atlas.readthedocs.io/en/v2.8.0/usage/output.html#genomes) 
+
+
+
+
+
+
+
+