- recipe kofamscan
KofamKOALA assigns K numbers to the user's sequence data by HMMER/HMMSEARCH against KOfam
KofamKOALA assigns K numbers to the user's sequence data by HMMER/HMMSEARCH against KOfam (a customized HMM database of KEGG Orthologs (KOs)). K number assignments with scores above the predefined thresholds for individual KOs are more reliable than other proposed assignments. Such high score assignments are highlighted with asterisks '*' in the output. The K number assignments facilitate the interpretation of the annotation results by linking the user's sequence data to the KEGG pathways and EC numbers.
- package kofamscan¶
While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.
Given that you already have a conda environment in which you want to have this package, install with:
mamba install kofamscan and update with:: mamba update kofamscan
To create a new environment, run:
mamba create --name myenvname kofamscan
myenvnamebeing a reasonable name for the environment (see e.g. the mamba docs for details and further options).
Alternatively, use the docker container:
docker pull quay.io/biocontainers/kofamscan:<tag> (see `kofamscan/tags`_ for valid values for ``<tag>``)