[Question] Can you give it predetermined genes/proteins?

[jolespin]

For example if you have eukaryotic genomes with eukaryotic gene calls, can you use these instead of giving full genomes? If not, can this be an option in the future?

[Waschina]

Hi! Unfortunately, this is not possible yet, but we are currently working on this option. This will be part of a major update to improve performance (i.e. reducing runtime). I'll tag this issue when we add the option to the main branch.

[jolespin]

Is this feature available in the current version?

[Waschina]

Not yet. We have an experimental branch, where we are currently running tests with this options. We'll post updates here or in the duplicate issue #64 .

[Waschina]

With the latest gapseq version, you can now use a multi-protein fasta file as genome input.

Here's an example workflow:

# Reaction+Pathway prediction
gapseq find -p all -t Bacteria -m Bacteria -b 200 e_lenta.faa.gz

# Transporter prediction
gapseq find-transport -b 200 e_lenta.faa.gz

# Draft network reconstruction
gapseq draft -r e_lenta-all-Reactions.tbl -t e_lenta-Transporter.tbl -b pos -u 200 -l 100 -p e_lenta-all-Pathways.tbl

# Gapfill-medium prediction
gapseq medium -m e_lenta-draft.RDS -p e_lenta-all-Pathways.tbl -c "cpd00007:0"

# Gapfilling
gapseq fill -m e_lenta-draft.RDS -c e_lenta-rxnWeights.RDS -g e_lenta-rxnXgenes.RDS -b 100 -n e_lenta-medium.csv

Please note: When providing a protein fasta, you will need to set the taxonomic domain manually using the -t option. Similarly, you also need to specific, which biomass reaction is added in the draft reconstruction step using the option -b.

[jolespin]

Looking forward to it. Once you get this sorted out I'm going to add it into my metagenomics pipeline as a separate module.

Does this also work for microeukaryotes like diatoms and fungi?