This is just about orienting - not circularising

Orient bacterial chromosomes

• Bacterial chromosomes are usually oriented at the gene dnaA.
• Plasmids are often oriented at the gene repA.
• The tool Circlator will usually orient the main chromosome at dnaA and other contigs at the start of the middle-most gene.
• We can also give Circlator a file of a repA gene to use to orient any plasmids.

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

• Extract the contig from the multi-fasta assembly file.
• Give circlator a fasta file of the gene (e.g. repA).

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

Links

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