Orient bacterial chromosomes

Orient all contigs

The circlator option to use is “fixstart”

circlator fixstart <multi-fasta file of assembled contigs> <output prefix>

Orient a contig to a specific gene

circlator fixstart --genes_fa <fasta file of gene sequence> <fasta file of contig> <output prefix>

Circlator https://github.com/sanger-pathogens/circlator/wiki