Examples

This page provides minimal working command examples using the current CLI.

Read Processing

rolypoly filter-reads -i reads_R1.fq,reads_R2.fq -o filtered_reads/

Assembly

rolypoly assemble -id filtered_reads/ -o assembly_out/

Marker Search

rolypoly marker-search -i assembly_out/final_assembly.fasta -o marker_out/

Virus Mapping

rolypoly virus-mapping -i assembly_out/final_assembly.fasta -o virus_hits.tab --db all

End-to-End

rolypoly end2end -i reads_R1.fq,reads_R2.fq -o rp_e2e_out/