ini settings recomandation for plant genome

[mictadlo]

Hi,
Do you have any settings recommendation for tetraploid plant genome?

Thank you in advance.

Michal

[ilanshom]

Hi Michal,
HINGE doesn't currently have capability of phasing polyploid genomes, so we don't have specific recommendations for a tetraploid plant genome. But we suggest that you use
del_telomeres = 1 and aggressive_pruning = 1 to simplify the final assembly graphs. In order to use aggressive_pruning you will need to use the latest commit of HINGE and add your ini file as a fourth argument to hinge clip; so you would have

hinge clip ecoli.edges.hinges ecoli.hinge.list test nominal.ini

[jwasmuth]

Hi @ilanshom,
When I add the .ini at the end of hinge clip-nanopore, I get the following error

hinge clip-nanopore ecoli.edges.hinges ecoli.hinge.list demo giardia.ini

Traceback (most recent call last):
File "/home/jwasmuth/bioinformatics/HINGE/inst/bin/../lib/hinge/pruning_and_clipping_nanopore.py", line 1214, in
add_groundtruth(G,json_file,in_hinges,out_hinges)
File "/home/jwasmuth/bioinformatics/HINGE/inst/bin/../lib/hinge/pruning_and_clipping_nanopore.py", line 806, in add_groundtruth
mapping = ujson.load(json_file)
ValueError: Unexpected character found when decoding 'false'

It seems to refer to the json_file variable. When I print it, I get

<open file 'giardia.ini', mode 'r' at 0x7fb8fbda99c0>

Thanks for any advice you have.
James

[ilanshom]

Hi James,
I just updated hinge clip-nanopore, and it should now be able to read the ini file. Let me know if things work with the latest commit.

[jwasmuth]

Hi @ilanshom,
That worked too. Thanks!
I let you or the creator close this issue when appropriate. For what it's worth, I found the information about large genomes very useful and recommend adding it to a recipe list if one is planned.
Thanks again
James