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This is just about orienting - not circularising
The circlator option to use is “fixstart”
circlator fixstart <multi-fasta file of assembled contigs> <output prefix>
circlator fixstart --genes_fa <fasta file of gene sequence> <fasta file of contig> <output prefix>
Circlator https://github.com/sanger-pathogens/circlator/wiki