MIntO 2.2.0 stable release

We have added a couple of new functionalities (see Newly supported functionalities below). This required that we moved some config variables from one yaml file to another. Considering this as a not-so-small change in behavior, we have upgraded MIntO to v2.2.0

We also fixed a lot of bugs since v2.1.0. Outputs are still identical with v2.1.0 within 6-decimal precision, so these bugs were not producing wrong results. But v2.2.0 will give you a smoother experience.

Making a fresh installation?

Please see instructions in our Wiki page for installation

Upgrading from 2.0.0 or 2.1.0?

Please do the following from where you cloned MIntO from github.

git pull
git checkout tags/2.2.0

After this, please rerun dependencies.smk using the same command you ran previously. This should finish without any complaints. If it does not finish successfully, please submit an issue report on github.

Newly supported functionalities

• Taxonomic profile outputs from mapping reads to genomes in MAG and refgenome modes.
  • A standardized tabular output listing genomes and their taxonomic annotations together with their quantitative profiles. Users can process them to generate e.g., species profiles by grouping genomes from the same species.
• Co-assembly of samples using a newly defined variable COAS_factor. If it is absent, still defaults to older behavior of coassembling samples using MAIN_factor.
• Capable of handling sample names with underscore and more special characters in them. But please try to avoid extremely special special characters (e.g., single- or double-quotes, space, percentage sign) in sample names.

Changes/bug-fixes

• Moving taxonomic annotation
  • Adding taxonomic annotations to the genome profiles required that we move taxonomic annotation of genomes from mags_generation.smk to gene_annotation.smk
  • The above change also meant that configuration parameters for taxonomy moved from one yaml file to another.
• Removed BINSPLIT_CHAR from configuration
  • In order to support handling of underscore characters in sample names, we had to take full control of how sample names and contig names will be separated in fasta headers. Therefore, we remove the ability of users to configure BINSPLIT_CHAR. Not that someone would need to - we never needed to tinker with it. Hopefully, you wouldn't even notice this change.
• Simplified MAG/refgenome profile filenames
  • They are now more intuitively gene_abundances, genome_abundances, and contig_abundances. This also avoids having genome as a suffix somewhere later in the name.

What's Changed

• Bugfix number of lines in concatting individual annotation files by @jszarvas in #53
• Optional COAS_factor, more flexible sample names and tax. profile plotting by @jszarvas in #54
• Taxonomic profiles from read-mapping in MAG/refgenome modes; other bug-fixes and improvements by @microbiomix in #55
• Upgraded test script to use v2.2.0 when released by @microbiomix in #56

Full Changelog: 2.1.0...2.2.0