Question: Genome-guided transcriptome assembly to partial genome?
gravatar for p.whatmore
4.7 years ago by
p.whatmore0 wrote:

I am currently tasked with assembling a transcriptome for a plant species.

There is a published genome available for this species, which is around 70% complete.

Is it better to do a genome-guided assembly (say, using Trinity) using this partial genome, or to do a de-novo?

Is there another approach that may improve the genome - e.g. merging this 70% genome with the published genome of a similar species?

Are there any other specific issues that should be addressed (and if possible, how) when doing a genome-guided assembly with only a partial genome?


Thanks in advance


assembly rna-seq latest • 1.2k views
ADD COMMENTlink modified 4.7 years ago by h.mon30k • written 4.7 years ago by p.whatmore0
gravatar for h.mon
4.7 years ago by
h.mon30k wrote:

You could try the approach implemented by the PASA pipeline.

ADD COMMENTlink written 4.7 years ago by h.mon30k
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