SUPER-FOCUS specifications

Information


Unique identifier OMICS_10222
Name SUPER-FOCUS
Alternative name SUbsystems Profile by databasE Reduction using FOCUS
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Python
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


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Maintainer


  • person_outline Genivaldo Gueiros Z. Silva <>

SUPER-FOCUS article

SUPER-FOCUS citation

2018
PMCID: 5859664

[…] metagenomics is its ability to characterise the functional potential of metagenomes. again, the results of functional analysis were generally consistent between all three sequencing platforms, but super-focus did detect significant differences in three functions which were present at greater than 1% relative abundance within the kefir metagenome. such discrepancies suggest that results […]

SUPER-FOCUS institution(s)
Computational Science Research Center, San Diego State University, San Diego, CA, USA

SUPER-FOCUS review

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Johanna Nelkner

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Desktop
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.