Which is better: PacBio or Illumina for de novo transcriptome?


I am obtaining quotes for transcriptome sequencing. I see that researchers often use both PacBio and Illumina to obtain and correct their transcriptome, but I only have the funds to do one of these.

My aim is to produce a de novo assembly for a eukaryote with no reference genome - a protist with a very large genome.

There seems to be a lot of conflicting advice out there. I have been told that PacBio Iso-Seq is great for transcriptomes as it produces whole transcripts. I am puzzled about why it is recommended above Illumina for de novo assembly, as it seems that the high indel rate will make it difficult to predict and annotate genes. I am concerned that there will be a large number of genes that I will miss as they will have poor database matches.

The quotes that I have obtained are similar for PacBio and Illumina NextSeq (2 x 75 bp, 150 cycles).

Any advice or opinions would be welcome!

Thank you.






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