Transcriptome assembly with Ion Torrent PGM data

Question

[p.whatmore]

I've previously done de-novo transcriptome assemblies on Illumina data using Trinity.

Recently I was provided with some Ion Torrent data and asked to do an assembly, but I'm wondering if the differences between Illumina and Ion Torrent data requires a different approach. Can anyone who may have used the two techs advise me here?

The primary difference, as it seems to me, is the variable read length in Ion Torrent vs fixed read length in Illumina. How does this affect assembly? (and/or mapping or other RNA-Seq procedures, while I'm mentioning it)

As I said, I used Trinity to assemble Illumina data. Is there more appropriate assembler for Ion Torrent?

Thanks in advance

Answer 1

[Benn]

You can try MIRA. It can use data from many different platforms, such as Ion Torrent.