SUPER-FOCUS specifications

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

versioning

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No versioning.

SUPER-FOCUS support

Maintainer

  • Genivaldo Gueiros Z. Silva <>

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Publications

Institution(s)

Computational Science Research Center, San Diego State University, San Diego, CA, USA

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Johanna Nelkner's avatar image Johanna Nelkner's country flag

Johanna Nelkner

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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.

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