Key Dependencies

ViroConstrictor relies on several important libraries and tools to provide robust viral genome analysis.

System Requirements

ViroConstrictor requires Python 3.10 or higher and runs on Linux systems. macOS may work but is not extensively tested. Windows is not supported (use WSL or containers instead).

Core Dependencies

Snakemake - Workflow management and pipeline orchestration with parallel processing support

Biopython - Biological sequence analysis, FASTA/GenBank parsing, and format conversions

BioValid - Biological data validation for input files and sequences

Pandas - Data manipulation, samplesheet processing, and result aggregation

PyYAML - Configuration file handling and workflow parameter management

OpenPyXL - Excel samplesheet reading and writing support

Rich - Enhanced terminal output with colored formatting and progress bars

DRMAA - Grid computing integration for HPC cluster job submission (SLURM, LSF)

Workflow Tools

Minimap2 - Fast sequence alignment for mapping reads to reference genomes

Samtools - SAM/BAM file manipulation and processing

Pysam - Python interface for SAM/BAM file reading and writing

FastP - Quality control and adapter trimming for sequencing data

AmpliGone - Primer removal from amplicon-based sequencing data

TrueConsense - Consensus sequence generation from aligned reads

AminoExtract - Amino acid sequence extraction and translation from genomic features

FastQC - Quality assessment of sequencing data

MultiQC - Aggregated quality control reporting

BEDtools - Genomic interval operations and analysis