De novo genome assembly using Ion Proton data: which assembler do you recommend?

Question

[fhsantanna]

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?

[Irsan]

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...

Answer 1

[Renesh]

See this post for your answer.

[Renesh]

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

Answer 2

[mjeammet]

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.

[fhsantanna]

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