Waste water analysis using Freyja pipeline with Automation
**Tools required **
conda install -c bioconda bwa
conda install -c bioconda samtools
conda install -c bioconda freyja
To run the pipeline
- Give executable permission to freyja-run
chmod +x freyja-run
- Keep your FASTQ files in a directory
- Keep the reference in a directory eg: /home/SARS/*All the files .dict, .fasta, .amb, .ann, .bwt, .fai, .pac, .sa
To run the pipeline use ./freyja-run
Enter the reference genome path: Path to your directory eg: /home/SARS/SARSCoV2_genome.fasta
Enter the FASTQ directory path: Path to a directory containing FASTQ files (.gz) eg: /home/SARS/FASTQ/
Enter the output directory path: Path to get the results eg: /home/SARS/Result
**Please refer original github repository for this analysis **