breseq

Finds mutations in short-read DNA resequencing data

brewmacoslinux

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Computational pipeline for finding mutations in short-read DNA resequencing data

breseq

Analyze a single sample against a reference genome$ breseq -r reference.fasta reads.fastq

Run analysis with multiple read files and specify output directory$ breseq -r reference.fasta -o output_dir reads1.fastq reads2.fastq

Generate HTML output report after analysis completion$ breseq -r reference.fasta -o results reads.fastq && breseq-plot-gd results/output.gd