- Unique identifier:
- Software type:
- Restrictions to use:
- Programming languages:
- SUbsystems Profile by databasE Reduction using FOCUS
- Command line interface
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- Genivaldo Gueiros Z. Silva <>
No open topic.
(Silva et al., 2016)
SUPER-FOCUS: a tool for agile functional analysis of shotgun metagenomic data.
PMID: 26454280 DOI: 10.1093/bioinformatics/btv584
Computational Science Research Center, San Diego State University, San Diego, CA, USA
1 user review
1 user review
Very nice tool to identify RAST subsystems in metagenomic whole community shotgun data. Also comes with R scripts for plotting the data: https://github.com/metageni/SUPER-FOCUS/tree/master/plotting_output
Therefore you need the stamp output format, it is created when you run all your samples in the same command. Only thing I disliked is the ".xls" output format which is not xls but csv, had to adjust the R scripts, also the used color palette since I had more samples than colors defined in the superfocus_functions.R script. Maybe this can be improved.
You can screen the stamp output csv for specific Subsystems present in the metagenome using a spreadsheet program or command line (my output files were too big for spreadsheet programs), enabling you to find the relevant biological features of your microbial community.