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The best factors to evaluate the quality of de novo transcriptome assembly

Hi everybody,

There are different criteria to evaluate de novo transcriptome assembly quality, which all of them have their pros and cons. What are the best and time-consuming way to assess quality of de novo transcriptome assembly to make a reliable transcriptome assembly. Please share me your experiences, any comments warmly welcomed. thanks

sequencing assembly rna-seq
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updated by Ram Ram • written by seta seta

2 answers

Transrate analyses a transcriptome assembly in three key ways:

  1. by inspecting the contigs themselves
  2. by mapping reads to the contigs and inspecting the alignments
  3. by aligning the contigs against proteins from a related species and inspecting the alignments

By far the most useful metrics are those based on read mapping, in particular you should pay attention to the Transrate score and the individual contig scores.

If you've got Ruby v2.0.0 or later, install Transrate with the command: $ gem install transrate

I have not tested transrate yet, but it is high on my 2015 Todo list.

• 0 views • link
updated by Ram Ram • written by rtliu rtliu

Hi rtliu,

Many thank for your response. It sounds great, is there anybody who tried this tool?

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updated by Ram Ram • written by seta seta

If a truly de novo transcriptomic assembly in an organism lacking of reference genome needs to be evaluated, test Detonate

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written by Antonio R. Franco Antonio R. Franco

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