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

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?

ion-proton assembly iontorrent
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updated by Ram Ram • written by fhsantanna fhsantanna
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...
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written by Irsan Irsan

2 answers

See this post for your answer.

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updated by Ram Ram • written by Renesh 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)

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written by Renesh Renesh

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.

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written by mjeammet • mjeammet

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

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written by fhsantanna fhsantanna

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