[mira_talk] megahubs
- From: Jose Huguet Tapia <jch63@xxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Wed, 25 Jun 2014 10:34:35 -0400
Mira users,
I am using MIRA 4 to assembly an Oomycete (Eukaryotic). I believe that the
organism has a highly heterozygous genome. I run a "first test" in MIRA
with Pacbio corrected Long reads. The assembly was going ok until I got the
message of megahubs. From previous discussion I learned that megahubs are
quite common in eukarotycs.
My concern is the level of total megahubs . It is more than 90 %. In the
message It says that I set the a maxium allowed ratio of 90. I believe that
I did not set this parameter though. Does MIRA 4 have a default for this.
I am ccing the message. Any comment is welcome
Thanks
Jose
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Hits chosen: 42589060
Localtime: Tue Jun 24 16:18:52 2014
Total megahubs: 143613
MIRA has detected megahubs in your data.This may not be a problem, but most
probably is, especially for eukaryotes.
You have more than 90% of your reads found to be megahubs.
You should check the following:
1) for Sanger sequences: are all the sequencing vectors masked /
clipped?
2) for 454 sequences: are all the adaptors masked / clipped?
You will find in the info directory a file called
'*_info_readrepeats.lst',
consult the MIRA manual on how to extract repeat information from there.
*ONLY* when you are sure that no (or only a very negligible number) of
sequencing
vector / adaptor sequence is remaining, try this:
3) for organisms with complex repeats (eukaryots & some bacteria):
- reduce the -HS:nrr parameter (divide by 2)
*ONLY* if the above fails, try increasing the -SK:mmhr parameter
Note that the number of present megahubs will increase computation time in
an exponential way, so be careful when changing -SK:mmhr.
You have 99.0353% of your reads as megahubs.
You have set a maximum allowed ratio of: 90
Ending the assembly because the maximum ratio has been reached/surpassed.
... [50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%]
....
|.
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