Question: Tools For De Novo Transcriptome Assembly Of Ion Torrent Reads?
2
gravatar for Ahdf-Lell-Kocks
7.5 years ago by
Ahdf-Lell-Kocks1.6k
Ahdf-Lell-Kocks1.6k wrote:

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.

denovo transcriptome • 5.1k views
ADD COMMENTlink written 7.5 years ago by Ahdf-Lell-Kocks1.6k
2
gravatar for Neilfws
7.5 years ago by
Neilfws48k
Sydney, Australia
Neilfws48k wrote:

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.

ADD COMMENTlink written 7.5 years ago by Neilfws48k

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.

ADD REPLYlink written 7.5 years ago by Ahdf-Lell-Kocks1.6k

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

ADD REPLYlink written 7.5 years ago by Neilfws48k

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.

ADD REPLYlink written 7.5 years ago by lexnederbragt1.2k

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.

ADD REPLYlink written 7.5 years ago by lexnederbragt1.2k
2
gravatar for Ahdf-Lell-Kocks
7.4 years ago by
Ahdf-Lell-Kocks1.6k
Ahdf-Lell-Kocks1.6k wrote:

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
ADD COMMENTlink written 7.4 years ago by Ahdf-Lell-Kocks1.6k
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