gapseq
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jotech
Informed prediction and analysis of bacterial metabolic pathways and genome-scale networks
The installation for gapseq requires root access to the machine which is often not the case for servers. It would be awesome if there was a conda package to facilitate...
For most `gapseq` subcommands, there is no way of designating the output path
> for bug reports and errors please report the output of: ./gapseq test Thank you for your work, this is a very move towards genome based metabolic modelling. For bacterial...
Hi again! I noticed while doing some testing of gapseq that it seems to run tblastn iteratively over the reference set. Would it be possible to change it so your...
Hi, As the title of your article said, gapseq could be used for the prediction of bacterial metabolic pathways. But I still would like to know whether this tool can...
Dear @jotech, Thank you for developing gapseq. I tried it, however, I have only protein fasta files which I think are incompatible right now. Do you plan to add support...
I am running the gapseq on a metagenomically assembled genome, and I am getting most of the out files, but I also see some warnings ? Should I be concerned...
While trying to investigate #149, I noticed that the same input files will generate slightly different results. This includes different reactions added during gapfilling, different predicted growth rates, and different...
Hi, I wonder how I can troubleshoot the following errors when adding certain pathways to my genome-scale models of interest. I am trying to add chlorobenzene degradation pathways to a...
> for bug reports and errors please report the output of: ./gapseq test Hi I am now test-running a gapseq with the following command conda activate Gapseq ; Tool="/home/sandia/softwares/gapseq/gapseq" ;...
