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!