A pangenomics pipeline tailored for arboviruses.
The pipeline only supports conda environments at the moment.
nextflow run mbbu/arbopan -profile conda --input "sample_data/*.fa" --results "sample_results" -r main
- 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 andbgzip
for zipping.