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Commit 6ed7d968 authored by Laura Denies's avatar Laura Denies
Browse files

Update README.md

parent 06d1a76c
......@@ -33,14 +33,7 @@ Clone the repository and its sub-modules:
# activate git lfs
git lfs install
# clone branch incl. sub-modules
git clone -b master --recursive https://git-r3lab.uni.lu/laura.denies/PathoFact.git
```
Perform futher installation/configuration steps:
```bash
# run set-up script
./set-up.sh
git clone -b PathoFact_updates --recursive https://git-r3lab.uni.lu/laura.denies/PathoFact.git
```
## Pipeline environment
......@@ -69,11 +62,14 @@ After the installation, adjust the path for this tool in `config.yaml` (keyword
## Input files
Each sample should have three input files:
Each sample should have one input file:
- `*.fna`: FASTA file containing nucleotide sequences of the contigs
- no whitespaces in FASTA headers
- for prediction of mobile genetic elements
- for prediction of mobile genetic elements and input for prodigal
The following files are generated by PathoFact itself:
- `*.faa`: FASTA file conatining translated gene sequences, i.e. amino acid sequences
- no whitespaces in FASTA headers
- for prediction of toxins, virulence factors and antimicrobial resistance genes
......@@ -81,8 +77,8 @@ Each sample should have three input files:
- no header, one gene ID per line
- contig and gene IDs should be the same as in the FASTA files
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.faa` and `SAMPLE_A.contig` for sample `SAMPLE_A`.
The input file for each sample should be located in the same directory.
For each sample, the corresponding input files should have the same basename, e.g. `SAMPLE_A.fna` for sample `SAMPLE_A`.
**NOTE**: For preprocessing and assembly of metagenomic reads we would suggest using IMP (https://imp.pages.uni.lu/web/)
......
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