FCMM is a pipeline for top-k based functional characterization of multiple metagenome samples to infer the major functions as well as their quantitative scores in a comparative metagenomics manner.
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Source code (Current version is v2.0.0) download
1. System requrements
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- Perl (v5.10.1)
- awk (GNU awk 3.1.7)
- sed (GNU sed 4.2.1)
- BWA (v0.7.10)
- DIAMOND (v0.7.8.57)
- Trimmomatic (v0.33)
2. Install
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>tar xvf fcmm_v2.0.0.tar
>cd fcmm_v2.0.0
>./configure.pl
3. Run
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>fcmm [module] [parameter file]
4. Module description
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[makedb]
makedb module is for making database from reference sequence files. DNA sequences or protein sequences are used to be a reference. RefSeq protein or RefSeq CDS are used for analyses using FCMM.
- RefSeq protein download
- RefSeq CDS download
[makeAn]
makeAn module is for makgin annotation files to be used in single sample analyses of FCMM. The required data files can be obtained from the links described below.
- GFF download
- ID mapping download
- GO download
[single]
single module is for single sample analyses.
[multi]
multi module is for a multi-sample anlsysis.
5. Parameter file
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The details of pameter file are descripbed in 'ex_parameter.txt' file in the source code.
6. Example workflow
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>./fcmm makedb param.txt
>./fcmm makeAn param.txt
>./fcmm single param.txt
>./fcmm multi param.txt
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