Setting parameters for MaSuRCa
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5.2 years ago
Ric ▴ 360

Hi, I have only Illuming paired-end reads form 2.5 Gbp plant genome.

#this parameter is useful if you have too many jumping library mates. Typically set it to 60 for bacteria and 300 for the other organisms 
LIMIT_JUMP_COVERAGE = 300

and

#set cgwErrorRate=0.25 for bacteria and ANY assembly containign PACBIO data and 0.1<=cgwErrorRate<=0.15 for other organisms.
CA_PARAMETERS =  cgwErrorRate=0.25

What would be the best way to set LIMIT_JUMP_COVERAGE and CA_PARAMETERS?

Thank you in advance.

Mic

Assembly masurca • 948 views
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