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?


1 Answer 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:


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


Your Answer

By clicking “Post Your Answer”, you agree to our terms of service and acknowledge you have read our privacy policy.

Not the answer you're looking for? Browse other questions tagged or ask your own question.