<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>

CC BY-SA 4.0
2021-05-12T02:11:27.020Z
2021-05-12T02:11:27.020Z
gringer
<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>

<assembly><transcriptome><pacbio>
What is the current state-of-the-art in assembling hybrid transcriptomes?
# 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

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## 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


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