Question: De novo genome assembly using Ion Proton data: which assembler do you recommend?
0
gravatar for fhsantanna
4.7 years ago by
fhsantanna440
Brazil
fhsantanna440 wrote:

I have four bacterial genomes that were sequenced using Ion Proton. The problem is they were not pairend sequenced, although there are dozens of reference genomes available for the species in question (Burkholderia and Bradyrhizobium).

What pipeline do you recommend to do a de novo genome assembly with these data? What is the best assembler in your opinion? 

assembly ion proton iontorrent • 2.5k views
ADD COMMENTlink modified 3.0 years ago by Biostar ♦♦ 20 • written 4.7 years ago by fhsantanna440
Why not use all of them? Because it takes time and effort to install and run them? Its not that hard to do so and if you think it is, it is a good training for you in Linux skills. Also, using different assemblers will force you to think how you define what is a good assembly and what is the difference between these programs. It can be very context dependent on what assembler is best...
ADD REPLYlink modified 4.2 years ago • written 4.2 years ago by Irsan7.0k
1
gravatar for Renesh
4.7 years ago by
Renesh1.7k
United States
Renesh1.7k wrote:

 

See this post http://seqanswers.com/forums/showthread.php?t=36165 for your answer

ADD COMMENTlink written 4.7 years ago by Renesh1.7k

You can use AbySS, Velvet or SOAPdenovo. I have tried ABySS before for plant genome assembly and its better than others (among open-source)

ADD REPLYlink written 4.7 years ago by Renesh1.7k
0
gravatar for mjeammet
4.2 years ago by
mjeammet0
France / Jouy-en-Josas / INRA
mjeammet0 wrote:

I guess you made a choice already but ...

What about SPAdes? Never used it myself but my team have been using it for a few assemblies and it seems to yield pretty reliable results.

ADD COMMENTlink modified 4.2 years ago • written 4.2 years ago by mjeammet0

Yes, I utilized SPADES. However the assembler with the best performance for Ion data was Mira.

ADD REPLYlink written 4.1 years ago by fhsantanna440
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