text: user235: 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 cogent. 
  Would this be considered a reasonable pipeline or is there an alterative recommendation?
  
  user73: My recommendation would be to run Trinity using the --long_reads option, which allows you to provide an error-corrected fastq file for anchoring reads to a transcript isoform. The reads are then clustered per-isoform, and assembled, in a similar fashion to what's done with genome-guided Trinity:
  https://github.com/trinityrnaseq/trinityrnaseq/wiki/Running-Trinity
  Trinity --seqType fq --max_memory 50G --long_reads corrected_pacbio_reads.fa --left reads_1.fq  --right reads_2.fq --CPU 6
  
  Disclaimer: I have contributed code to Trinity at some time in the distant past
  
original_text: 235: <p>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. </p>
  
  <p>One example I saw (<a href="https://www.nature.com/articles/celldisc201731" rel="nofollow noreferrer">Li et al 2017</a>), used the standard PacBio tools to assemble a transcriptome, followed by correcting the assembled sequence using a tool called <code>proovread</code>, followed by <code>cd-hit-est</code> and then <code>cogent</code>. </p>
  
  <p>Would this be considered a reasonable pipeline or is there an alterative recommendation?</p>
   73: <p>My recommendation would be to run <em>Trinity</em> using the <code>--long_reads</code> option, which allows you to provide an error-corrected fastq file for anchoring reads to a transcript isoform. The reads are then clustered per-isoform, and assembled, in a similar fashion to what's done with genome-guided Trinity:</p>
  <p><a href="https://github.com/trinityrnaseq/trinityrnaseq/wiki/Running-Trinity" rel="nofollow noreferrer">https://github.com/trinityrnaseq/trinityrnaseq/wiki/Running-Trinity</a></p>
  <pre><code>Trinity --seqType fq --max_memory 50G --long_reads corrected_pacbio_reads.fa --left reads_1.fq  --right reads_2.fq --CPU 6
  </code></pre>
  <p><em>Disclaimer: I have contributed code to Trinity at some time in the distant past</em></p>
  