NGS Analyzer is a comprehensive python-based pipeline designed for amplicon-based NGS data analysis. It streamlines processes such as demultiplexing, read alignment, variant calling, and annotation, providing researchers with a powerful tool for genomics research.
python -m pip install -r requirements.txtC:\Path\To\Python\python.exe -m pip install -r requirements.txtOr, if python is in your PATH environment varriable,
python.exe -m pip install -r requirements.txtThe project also relies on several external tools. Please ensure these are installed and their paths in your configuration.
bcl2fastq2 | Converts Illumina BCL files to FASTQ files.
bwa-mem2 | Fast aligner for sequencing reads.
Trimmomatic | Read trimming tool.
pTrimmer | Adapter trimming and quality control.
Picard | Toolkit for manipulating high-throughput sequencing data.
Genome Analysis Toolkit | Genome Analysis Toolkit for variant discovery.
samtools | Utilities for manipulating alignments and variant calling.
bedtools | Genomic interval manipulation.
SnpEff | Variant annotation and effect prediction.
Pisces | Variant caller optimized for amplicon sequencing.
Annovar | Variant annotation tool.
Please follow the official installation instructions for each tool required for your needs to ensure proper setup.
Contributions are welcome! Please open issues or pull requests.
Currently in development. See the project documentation at readthedocs.