Question: De Novo Transcriptome Assembly Options For Mixed Platforms (454, Sanger, Solexa)
2
gravatar for Jlw
7.5 years ago by
Jlw180
USA/Storrs/UConn
Jlw180 wrote:

Looking for some information on assemblers that can work with mixed data for de novo assembly of transcriptomes

I currently have independent assemblies of RNA-Seq data (normalized, processed, and assembled with trinity), 454 data (processed and assembled with newbler), and some older Sanger EST data.

When looking at co-assembly/hybrid options (non-commercial only), the only one that seems specifically able to handle multiple platforms is Mira.

Others that do, Celera, etc. seem to only be applicable for genome assemblies.

Any advice on other packages that I have missed or other preferred approaches?

ADD COMMENTlink modified 4.6 years ago by Biostar ♦♦ 20 • written 7.5 years ago by Jlw180
1

I haven't tried other options, but Mira worked well for us, with Solexa, Sanger and 454 mixed inputs

ADD REPLYlink written 7.5 years ago by Israel Barrantes740

I am very much interested in answers to this question.

ADD REPLYlink written 7.5 years ago by 2184687-1231-83-5.0k

My experience with Mira is that it is a huge resource hog. To assemble any appreciable amount of data, you will need a lot of memory. But that may be the only option for your data.

ADD REPLYlink written 7.5 years ago by Daniel Standage3.9k

Wonderful, thanks! Mira is indeed a resource hog. It is sounding like MIRA is the way to go for now!

ADD REPLYlink written 7.5 years ago by Jlw180
0
gravatar for rob234king
5.7 years ago by
rob234king580
UK/Harpenden/Rothamsted Research
rob234king580 wrote:

SOAPtrans I believe can use different data sets and can set priority too.

ADD COMMENTlink written 5.7 years ago by rob234king580
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