Greetings! It seems like a while (5 years) since this question was asked and I am sure there has been lots of progress on the topic in that time. I have a nice de novo assembly for a transcriptome from 125bp HiSeq paired-end reads and would like to go through and do an extra step of error correction on the assembly. I'm interested to hear what you experiences have been, positive and negative, with error correction software and methods. Many thanks.
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Post assembly error correction? I am not sure if this is done, at least not on an automated basis. Certainly people will annotated the assembly and perhaps throw away transcripts that do not annotate or annotated poorly. Mapping the reads back to the assembly and making cut-offs based on that has a high chance of throwing away biologically-true assemblies. Correcting the bases themselves seems like something best done pre assembly. -
There are some tools for this, such as FinisherSC:
Not sure how that would work on transcriptomes, though.Comment
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