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Welcome to Pathotypr - Select a tool to get started

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Welcome to Pathotypr

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A comprehensive toolkit for genome classification and variant genotyping using k-mer based methods.

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Load M. tuberculosis markers & reference genome. Pathotypr works with any organism.

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+ Pathotypr Workflow Scheme +
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Need help? Check the tooltips (?) next to each field for detailed explanations.

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Supports FASTA, FASTQ, TSV, and GFF formats. Drag & drop or click to select files.

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Input Data

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Click to select or drag file here
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.fasta, .fa, .fna
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Output

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Parameters

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Input Files

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Click to select or drag file here
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.fasta, .fa, .fna
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Click to select or drag file here
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.pathotypr.zst
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Output

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Options

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Reference & Markers

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Click to select or drag marker files here
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.tsv, .txt — multiple files supported
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Click to select or drag file here
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.fasta, .fa, .fna
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Input Genomes

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Click to select or drag files here
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One or more FASTA files
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Click to select or drag files here
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.gff, .gff3 (matched by filename)
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Output

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Options

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Reference & Markers

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Click to select or drag file here
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.fasta, .fa, .fna
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Input Reads

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Click to select or drag files here
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FASTQ files (multiple allowed)
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Output

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Options

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References

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Click to select or drag file here
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Multi-FASTA with reference genomes
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Input Reads

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Click to select or drag files here
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FASTQ files to match
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Output

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Options

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Recommended for most runs: keep Strict percentages enabled for results consistent with previous analyses.

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Use advanced speed options only when you want faster runtime and can accept potential score changes.

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+ + Advanced speed options (optional) + ?These options are applied only when Strict percentages is disabled. + +
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+ If you need strict reproducibility with old reports, keep Strict percentages enabled and leave advanced options untouched. +
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