SUPER-FOCUS pipeline

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


Add your version

Maintainer


  • person_outline Genivaldo Gueiros Z. Silva <>

Publication for SUbsystems Profile by databasE Reduction using FOCUS

SUPER-FOCUS IN pipelines

 (3)
2018
PMCID: 5859664
PMID: 29554948
DOI: 10.1186/s40168-018-0437-0

[…] with greater sequencing depth. notably, panphlan detected the dominant strains in each kefir sample above 500,000 reads per sample. again, the outputs from functional profiling analysis using super-focus were generally accordant between the platforms at different sequencing depths. finally, and expectedly, metagenome assembly completeness was significantly lower on the miseq than either […]

2018
PMCID: 5859664
PMID: 29554948
DOI: 10.1186/s40168-018-0437-0

[…] 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 […]

2018
PMCID: 5859664
PMID: 29554948
DOI: 10.1186/s40168-018-0437-0

[…] sequencers cannot be reliably compared., above, we described a considerable difference in the compositional profiles determined by different species classifiers. hence, we also compared results from super-focus with those from humann2, which is an alternative tool for functional analysis of metagenomes. we observed a similarly pronounced disparity in the results generated by these methods. […]

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

SUPER-FOCUS review

star_border star_border star_border star_border star_border
star star star star star

Johanna Nelkner

star_border star_border star_border star_border star_border
star star star star star
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.