We are considering attempting de novo assembly of a species transcriptomes (i.e. without a reference genome) using the combined NGS outputs of Iso-seq and Illumina.
One example I saw (Li et al 2017), used the standard PacBio tools to assemble a transcriptome, followed by correcting the assembled sequence using a tool called
proovread, followed by
cd-hit-est and then
Would this be considered a reasonable pipeline or is there an alterative recommendation?