Commit eb4ce0e7 authored by Laura Denies's avatar Laura Denies
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Update README.md

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# PathoFact 1.0 (branch SpringClean) # PathoFact v1.0
PathoFact is an easy-to-use modular pipeline for the metagenomic analyses of toxins, virulence factors and antimicrobial resistance. PathoFact is an easy-to-use modular pipeline for the metagenomic analyses of toxins, virulence factors and antimicrobial resistance.
Additionally, PathoFact combines the prediction of these pathogenic factors with the identification of mobile genetic elements. Additionally, PathoFact combines the prediction of these pathogenic factors with the identification of mobile genetic elements.
...@@ -84,6 +84,8 @@ Each sample should have three input files: ...@@ -84,6 +84,8 @@ Each sample should have three input files:
The files should be located in the same directory. The files should be located in the same directory.
For each sample, the corresponding input files should have the same basename, e.g. `SAMPLE_A.fna`, `SAMPLE_A.fna` and `SAMPLE_A.contig` for sample `SAMPLE_A`. For each sample, the corresponding input files should have the same basename, e.g. `SAMPLE_A.fna`, `SAMPLE_A.fna` and `SAMPLE_A.contig` for sample `SAMPLE_A`.
**NOTE**: For preprocessing and assembly of metagenomic reads we would suggest using IMP (https://imp.pages.uni.lu/web/)
## Run PathoFact ## Run PathoFact
### Configuration ### Configuration
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