gmboowa/ASFV-ONT-Gen

ASFV-ONT-Gen is a pipeline for analyzing African Swine Fever Virus (ASFV) whole-genome sequencing data generated using Oxford Nanopore Technology (ONT). It supports genome assembly & assembly statistics, variant calling, annotation & phylogenetic analysis, enabling rapid genomic insights for surveillance & outbreak investigation # ASFV-ONT-Gen: A pipeline for African swine fever virus ONT whole-genome analysis **ASFV-ONT-Gen** is a modular pipeline for analyzing whole-genome sequencing data of *African Swine Fever Virus* (ASFV) using Oxford Nanopore Technologies (ONT). It covers preprocessing, assembly, annotation & phylogenetic analysis using a reference genome such as `NC_044959.2.fasta`. --- ## Features - **Swine sequence removal**: Hostile, accurate host read removal - **Quality control**: FastQC, NanoPlot, MultiQC - **Read mapping**: Minimap2 - **Taxonomic classification**: Kraken2 with viral database - **Assembly**: De novo (Flye + Medaka polish) & reference-based - **Variant calling & annotation**: BCFtools & SnpEff - **Multi-threading**: Efficient parallel processing - **Summary reports**: MultiQC, assembly stats, mapping summaries - **Phylogenetics**: MAFFT, IQ-TREE, and ggtree --- ### Pipeline workflow ## Installation ### Prerequisites - Conda - Java 21+ (for SnpEff) ### Hostile clean swine pipeline ## Dependencies Ensure these tools are installed in your environment: # Tool installation command ```bash # Install all dependencies in one command: conda create -n hostile_env -c bioconda ncbi-datasets-cli minimap2 hostile conda activate hostile Required arguments: Argument description | Option | Description | |------------------|---------------------------------------------------------------------------| | `--fasta` | NCBI accession (e.g., `GCF_000003025.6`) or path to existing FASTA file | | `-i`, `--input` | Text file listing paths to FASTQ files (one per line) | | `-o`, `--output` | Directory to store all results | Optional arguments: Argument default description | Option | Default Value | Description | |--------------------|---------------------|--------------- …