[mira_talk] megahubs in MIRA
- From: Isabelle Lesur <isabelle.lesur.kupin@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Tue, 20 Mar 2012 14:36:58 +0100
Hello,
I am trying to perform an assembly consisting of 84 086 Sanger reads
with qualities.
I used the following command:
-bash-3.2$ mira --project=OCV2_prime_full_length
--job=denovo,genome,normal,sanger --noclipping=all --notraceinfo
SANGER_SETTINGS
And the assembly stopped bacause of Megahubs.
Total megahubs: 8
I followed the recommandations MIRA gave me:
- I checked for vector/adaptor sequences
- I set the -SK:nrr parameter as follow:
-SK:nrr=10 and -SK:nrr=20 and -SK:nrr=30
The number of megahubs reached 66 with the -SK:nrr parameter
- I used the -SK:mmhr parameter
This time, the number of megahubs reached 74
I then used RepeatMasker to mask the repeats in my sequenced and
clipped all the Ns.
This time, I ended up with 66 megahubs....
So, does anybody know how I could get read off these megahubs???
Thank you for your help!
Isabelle
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