V2.8 - Toiminnot
This is a major update of metagenome-atlas. It was developed for the 3-day course in Finnland, that's also why it has a finish release name.
What is new?
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.
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.
Genecatalog
The command atlas run gene catalog 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
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 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.
