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## Input files
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Each sample should have one input file:
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- `*.fna`: FASTA file containing nucleotide sequences of the contigs
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- no whitespaces in FASTA headers
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- for prediction of mobile genetic elements and input for prodigal
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The following files are generated by PathoFact itself:
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- `*.faa`: FASTA file conatining translated gene sequences, i.e. amino acid sequences
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- no whitespaces in FASTA headers
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- for prediction of toxins, virulence factors and antimicrobial resistance genes
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- `*.contig`: TAB-delimited file containing a mapping from contig ID (1st column) to gene ID (2nd column)
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- no header, one gene ID per line
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- contig and gene IDs should be the same as in the FASTA files
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The input file for each sample should be located in the same directory.
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For each sample, the corresponding input files should have the same basename, e.g. `SAMPLE_A.fna` for sample `SAMPLE_A`.
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**NOTE**: For preprocessing and assembly of metagenomic reads we would suggest using IMP (https://imp.pages.uni.lu/web/)
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