Question: Is there any tool or script to evaluate transcriptome assembly quality in terms of accuracy, completeness, contiguity, and gene fusions?
5
gravatar for seta
4.0 years ago by
seta1.1k
Sweden
seta1.1k wrote:

Dear all,

I would like to assess the de novo assembled transcriptome of a non-model plant in terms of accuracy, completeness, contiguity, and gene fusions. Could you please share your tool or script to evaluate the above-mentioned parameters on assembled transcriptome? Your feedback would be greatly appreciated.

rna-seq alignment assembly • 2.0k views
ADD COMMENTlink modified 4.0 years ago by Richard Smith-Unna130 • written 4.0 years ago by seta1.1k
3
gravatar for Richard Smith-Unna
4.0 years ago by
UK
Richard Smith-Unna130 wrote:

Transrate (http://hibberdlab.com/transrate/) does these things.

You give it your assembly (or multiple assemblies) and the reads used to generate them, and it outputs a lot of summary statistics about the assembly. These include the accuracy and completeness of the assembly. It also evaluates each individual contig in the assembly, giving scores for various aspects of the contig quality, and a summary score called the contig score. Finally, it can automatically learn a contig score cutoff to discard low-quality contigs and output the subset of contigs that maximises the assembly score.

I'm one of the Transrate developers, so let me know if you have any trouble.

ADD COMMENTlink modified 4.0 years ago • written 4.0 years ago by Richard Smith-Unna130
1
gravatar for thackl
4.0 years ago by
thackl2.6k
MIT
thackl2.6k wrote:

Have a look at rnaQUAST. 'rnaQUAST is a tool for evaluating RNA-Seq assemblies using reference genome and annotation'.

ADD COMMENTlink written 4.0 years ago by thackl2.6k

Thanks, but as you also mentioned it works using reference genome and annotation. I expressed that my case is a non-model plant, no available genome and annotation. 

ADD REPLYlink written 4.0 years ago by seta1.1k

Ah, okay, I did not realize that non-model should imply lack of genome.
 

ADD REPLYlink written 4.0 years ago by thackl2.6k
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