Invalid Campylobacter jejuni assemblies

[samuelbloomfield]

Describe the bug
I have a problem running Socru on Campylobacter jejuni assemblies. The Campylobacter genome can be separated into three fragments separated by ribosomal operons. For Campylobacter coli, the origin of replication (Ori) is in fragment 3 and the terminus (ter) is in fragment 1, and Socru can easily be used to identify misassembles for this species. However, for Campylobacter jejuni Ori and Ter are both on fragment 1. Because of this, Socru always calls the assemblies invalid.

Campylobacter jejuni RED GS1.0 1 2 3 Invalid --> 1(Ori)(Ter) --> 2 --> 3
Campylobacter coli GREEN GS1.0 1 2 3 Valid --> 1(Ter) <-- 2 <-- 3(Ori)

In addition, the operon direction file always shows Ori and Ter in alphabetical order on fragment 1, making it difficult to determine if the assembly is valid using Socru. To test this I took a C. jejuni chromosome, determined its reverse compliment and placed it through Socru, and Ori was still before Ter on fragment 1.

Normal Campylobacter jejuni RED GS1.0 1 2 3 Invalid --> 1(Ori)(Ter) --> 2 --> 3
Reverse compliment Campylobacter jejuni RED GS1.0 1 2 3 Invalid <-- 1(Ori)(Ter) <-- 3 <-- 2

Therefore, if Ori and Ter are on the same fragment can Socru be changed to give the order of Ori and Ter as they appear on the fragment, and can it call C. jejuni assemblies with Ori and Ter on fragment 1 valid.