SEQanswers

Go Back   SEQanswers > Sequencing Technologies/Companies > Ion Torrent



Similar Threads
Thread Thread Starter Forum Replies Last Post
cuffmerge assembly vs denovo assembly of RNAseq data skm Bioinformatics 0 10-16-2013 10:16 PM
Iontorrent denovo and reference assembler tools pari_89 Bioinformatics 3 05-14-2013 07:47 AM
Pull CDS from EST assembly k-gun12 Bioinformatics 0 02-25-2013 05:36 PM
Removing homopolymer associated indels from EST assembly JackieBadger Bioinformatics 1 03-08-2012 09:12 AM

Reply
 
Thread Tools
Old 10-30-2013, 01:46 PM   #1
nareshvasani
Member
 
Location: NC

Join Date: Apr 2013
Posts: 57
Default Mira4 Assembler using all memory for denovo, est assembly

Hi Users,

My PC has 48 GB of RAM and 8 CPU. I am trying to create denovo assembly using Mira 4 Assembler. Input file has only 2 fastq files with only 30 million reads with sequence length 50-350 nt.

I used below manifest.comf file

project = miraproject job = est, denovo, accurate
parameters = COMMON_SETTINGS -GENERAL:number_of_threads=4 amm=off -HS:mnr=yes:nrr=8
parameters = IONTOR_SETTINGS -CL:qc=no -ALIGN: min_relative_score=90 -ASSEMBLY:minimum_read_length=200

readgroup = SomeUnpairedIonTorrentReadsIGotFromTheLab
technology = iontor
data = /media/DATAPART3/Combine_Files/miraproject/data/


But problem is it is taking long time more than 20 hours and it is using all the memory.

Any suggestion?


I would really appreciate your help.

Thanks in advance.
Naresh
nareshvasani is offline   Reply With Quote
Old 11-06-2013, 08:36 AM   #2
nareshvasani
Member
 
Location: NC

Join Date: Apr 2013
Posts: 57
Default

Hi Users,

bump....
nareshvasani is offline   Reply With Quote
Old 11-06-2013, 09:35 AM   #3
sklages
Senior Member
 
Location: Berlin, DE

Join Date: May 2008
Posts: 628
Default

You should post the issue on the mira mailing list.
sklages is offline   Reply With Quote
Old 01-28-2014, 12:02 PM   #4
akorobeynikov
Member
 
Location: Saint Petersburg, Russia

Join Date: Sep 2013
Posts: 25
Default

You may also consider SPAdes 3.0, which contains experimental IonTorrent error correction and assembly module.
akorobeynikov is offline   Reply With Quote
Old 01-28-2014, 01:25 PM   #5
nareshvasani
Member
 
Location: NC

Join Date: Apr 2013
Posts: 57
Smile SPAdes

Hi akorobeynikov,

Thanks for your reply. I am doing transcriptome analysis and SPAdes is useful for only genome analysis.
Am i right?

Best,
Naresh




Quote:
Originally Posted by akorobeynikov View Post
You may also consider SPAdes 3.0, which contains experimental IonTorrent error correction and assembly module.
nareshvasani is offline   Reply With Quote
Old 01-28-2014, 01:26 PM   #6
nareshvasani
Member
 
Location: NC

Join Date: Apr 2013
Posts: 57
Smile

Hi sklages,

I contacted them, they just told me get new computer resources with more GB on it.

Thanks,
Naresh


Quote:
Originally Posted by sklages View Post
You should post the issue on the mira mailing list.
nareshvasani is offline   Reply With Quote
Old 01-28-2014, 02:08 PM   #7
akorobeynikov
Member
 
Location: Saint Petersburg, Russia

Join Date: Sep 2013
Posts: 25
Default

Quote:
Originally Posted by nareshvasani View Post
Thanks for your reply. I am doing transcriptome analysis and SPAdes is useful for only genome analysis.
Am i right?
Well, I never did this by myself, but rumors are that you still
may try to assemble them in single-cell mode. I'd select the standard set of kmers, that is - 21,33,55
akorobeynikov is offline   Reply With Quote
Old 01-28-2014, 03:08 PM   #8
danwiththeplan
Member
 
Location: Auckland

Join Date: Sep 2011
Posts: 72
Default

Try a less memory-heavy assembler that is based on de bruijn graphs (eg Trinity, transABYSS)? I think Mira is based at least partially on overlap-layout-consensus so will be very memory hungry. If you have 30 million reads, this line from the Mira4 manual may be relevant:

Quote:
1.4. For which data sets to use MIRA and for which not

As a general rule of thumb: if you have an organism with more than 100 to 150 megabases or more than 20 to 40 million reads, you might want to try other assemblers first.
danwiththeplan is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 02:26 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO