mass23/nomis_ensemble

nomis_ensemble's Issues

ROCK: Co-assembly

To do:

• Co-assembly of ROCK samples

ROCK: Metabolic insights

To do:

• FUNCs
• METABOLIC

ROCK: Inter-kingdom metabolic interaction

To do:

• Euk + prok + viruses interactions based on gene abundance

Fasta files for training/testing the data?

Looking forward to collaborating on this! I just forked over the repo. I'm having trouble finding the fasta files used for training/testing the models.

Is the main goal to classify Eukaryotic contigs vs. everything else or Euk vs. Bac vs. Arc vs. Virus?

ROCK: Cold-adaptation genes

To do:

• Build database
• Comparative genomics for bins
• Comparative genomics for metagenomes

Input error for `Eukaryotic binning Snakefile`

@michoug

• line #278 has a directory as input in the Euk binning Snakefile

• Leads to errors, 'cos snakemake doesn't take folders as input

• Please add a file that is typically found in the folder to the line so we can use the the dirname variable.

EukProClassifier

we need to implement the classifier with the khmer library

EUCI: Unannotated clusters

• Purpose: Generate statistics for unannotated clusters
• To identify clusters that are truly "known unknowns" from those that are "unknown unknown"

Todo:

• BLAST
• tRNA
• Cluster identity
• Cluster GC
• Coverage

Eukrep comparison

To compare our method against the Eukrep

• Compring the different methods,
• Comparing data transformation
• Comparing running time
• Comparing k-mer sizes

ROCK: Metabolic network interaction

To do:

• FUNCs networks
• Shared metabolic niches

ROCK: Quality and Taxonomy

To do:

• CheckM
• GTDBtk

ROCK: Eukaryotes

To do:

• Classification via BUSCO for NA bins
• EukRep
• EUKElele
• Binning from #8