mdmcleaner
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KIT-IBG-5
MDMcleaner the assessment, classification and refinement tool for microbial dark matter SAGs and MAGs
maybe base nucleotide comparisons on minhash instead of blast searches? Maybe use sourmash for this? [https://sourmash.readthedocs.io/en/latest/](https://sourmash.readthedocs.io/en/latest/)
maybe use 98% aminoacid identity cut-off? proteins that are unique for one species in a genus would still be attributed to that individual species (but only one copy would be...
sometimes, when the gtdb databse is updated, it can happen that the representative genome of a species changes. if a process was started with one database, and then finished with...
implement lock files to prevent two users writing to the same results-folder at the same time. - [ ] lock file for database creation - [ ] lock file for...
ORF calling on eukaryotes functions drastically different than for bacteria. Instead of using Eukaryotic proteins as references, rather run prodigal with prokaryotic and metagenomic settings on reference Eukaryotic genomes (not...
Divide protein blast databases into smaller subsets (similar to nucleotide dbs). possibilities: 1. seperate by component sub-db (gtdb or refseq_eukaryote/virus) 2. seperate into roughly equal numbers of proteins - [...
add workflows to: - [ ] classify all contigs of a large shotgun metagenome (blast contigs in portions so progress can be saved in between) - [ ] reuse shotgun...