check if one unitig is truly circual

Question

[orange]

For bacteria assembly with pacbio reads, a unitig is easy at most time. But how to check if it is truly circular?

I tried CA_best_edge_to_GML.py, and an error happen like

Traceback (most recent call last):
File "CA_best_edge_to_GML.py", line 51, in 
id1, lib_id, best5, o1, best3, o3 = l
ValueError: too many values to unpack

So I changed line 51 to id1, lib_id, best5, o1, best3, o3 = l[:6], and line 51 works, but another error happens:

Traceback (most recent call last):
File "CA_best_edge_to_GML.py", line 52, in 
G.add_node(id1, unitig="utg%s" % frg_to_tig[id1])
KeyError: '8'

So how to solve it? Or any other way to check if contig is truly circular?

Thanks!

Answer 1

[rhall]

For an up to date Celera to Gephi script:

https://github.com/PacificBiosciences/Bioinformatics-Training/blob/master/scripts/CeleraToGephi.py

General circularization and trimming:

https://github.com/PacificBiosciences/Bioinformatics-Training/wiki/Circularizing-and-trimming

Video how to:

http://files.pacb.com/Training/CircularContigConfirmationGepard/story.html