Tools For De Novo Transcriptome Assembly Of Ion Torrent Reads?

Question

[Ahdf-Lell-Kocks]

I've seen on Ion Torrent's developers site that people is using MIRA as a de novo assembler of Ion Torrent RNA-seq datasets. I am interested in knowing if there is any other software out there that could do a good job at it.

NOTE: Not interested in mapping RNA-seq reads to the genome, just strictly de novo assembly of RNA-seq reads, as one would do with Trinity for Illumina data.

Answer 1

[Neilfws]

Suggest you start at the SEQanswers wiki software hub, where you can browse and narrow down software by technology (e.g. Ion Torrent) and application (e.g. assembly).

When I do that, I get 5 results (including MIRA). As to whether they do a "good job" - you'll have to do a little more research, I have no direct experience with them.

[Ahdf-Lell-Kocks]

Out of the list of 5 in the SEQanswers wiki, I can confirm MIRA claims to be able to do it, but I couldn't confirm it for any of the other 4 in the list.

[Neilfws]

Why not? They all list Ion Torrent under "Technology" and assembly under "application domain" in the Application Data table, right side of screen.

[lexnederbragt]

Now you get 6 results, as I added Ion Torrent to the newbler software. Using newbler for transcriptome assembly with Ion Torrent data should not be a problem, but I don't know if anyone has tried this yet.

[lexnederbragt]

Now you get 6 results, as I added Ion Torrent to the newbler software. Using newbler for transcriptome assembly with Ion Torrent data should not be a problem, but I don't know if anyone has tried this yet.

Answer 2

[Ahdf-Lell-Kocks]

Answering my own question, I have tried two tools for a 316 human transcriptome dataset:

Mira

id=hsa.rnaseq.UHR
ln -s $id.fastq ${id}_in.iontor.fastq
mira --project=$id -DI:trt=/tmp/ --job=denovo,est,accurate,iontor IONTOR_SETTINGS -LR:mxti=no

Seqman Ngen (trial version)

Select de novo transcriptome of Ion Torrent reads, generate script file.
~/seqman_ngen/usr/bin/smng hsa.rnaseq.ngen.all.script