metaspades

[Biofarmer]

Hi,
May I ask whether it is possible to set the parameter (--only-assembler) for metaSPAdes due to the issue as below link?
ablab/spades#152

Thank you.

[ursky]

I don't want to make this a general option, but it would be very easy for you to modify the assembly.sh script within metawrap to include this option.

[Biofarmer]

Thank you for your answer. I am not sure how to modify the assembly.sh which has been installed in our cluster?

[ursky]

One way would be to obtain your own copy of the script here: https://github.com/bxlab/metaWRAP/tree/master/bin/metawrap-modules, and modify it, and then just run this script instead. So instead of metawrap assembly -h, try ./myfolder/assembly.sh -h. Should work.

[davidbio]

I have been reading about this recommendation because we also have a dataset where some samples apparently never finish. They take 10 days on a 48 cores machine (without finishing), whereas with only-assembler they finish in 40 minutes.

What does CQF stand for?
How does SPAdes take into account the quality scores? I haven't seen any option that allows setting a threshold or similar.

If we ask the user to take care of sequence quality, can't we go for only-assembler without problems?