Length of circular contigs

[shamir-lab]

Length of circular contigs

[dpellow]

Hi Jakob - Thanks for your interest in the tool and the information. Is the mismatch 86 or a multiple of 86? What is the k-mer size?

[Russel88]

It is a multiple of 86, so either 86, 172, 258, etc..

I have a guess of where 86 comes from. The k-mer size is 141, so I set -k 141, the default k-mer size in your code is 55. 141 - 55 = 86

[dpellow]

Hi Jakob - thanks for bringing this bug to our attention. We've just updated the code and this issue should be fixed. Please reopen the issue if you still see this problem after the update.

Thanks!

[Russel88]

Thank you for the fast reply. Although, now I get this error:

File "build/bdist.linux-x86_64/egg/recyclelib/utils.py", line 289, in get_spades_type_name
File "build/bdist.linux-x86_64/egg/recyclelib/utils.py", line 133, in get_seq_from_path
TypeError: 'int' object has no attribute '__getitem__'

[dpellow]

OK thanks - should be fixed now.

[Russel88]

It works now.
Thank you!