Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2021-05-12T02:11:27.020Z
Answers.LastActivityDate: 2021-05-12T02:11:27.020Z
Answers.UserDisplayName: gringer
Body: <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>
  
Tags: <assembly><transcriptome><pacbio>
Title: What is the current state-of-the-art in assembling hybrid transcriptomes?
ThreadText: # What is the current state-of-the-art in assembling hybrid transcriptomes?
  
  (Asked by: username_0 on 2018-07-12)
  
  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](https://www.nature.com/articles/celldisc201731)), 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?
  
  **Tags:** assembly, transcriptome, pacbio
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2021-05-12. Score: 1
  
  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*
  
  
  ---
  
  