arbopan

A pangenomics pipeline tailored for arboviruses.

Usage

The pipeline only supports conda environments at the moment.

nextflow run mbbu/arbopan -profile conda --input "sample_data/*.fa" --results "sample_results" -r main

References

vgteam/vg: Variation graph toolkit.
GSLBiotech/mafft: Multiple sequence alignment tool.
sanger-pathogens/snp-sites: Rapidly extracts SNPs from a multi-FASTA alignment.
samtools/htslib: Provides tabix for indexing and bgzip for zipping.