Combining unpaired and paired-end reads in spades assembly

Question

[rescueson]

I have two fastq illumina files containing paired-end reads (forward, reverse) and one fastq pacbio file containing a non-paired end read. I would like to incorporate my non-paired end read into my paired-end read assembly using spades but continue to receive errors in my code.

spades.py --pe1-1 accession1-1.fastq --pe1-2 accession1-2.fastq --pe1-s accession2-1.fastq -o spades_output

Any input or references would be helpful.

[andres.firrincieli]

Did you check spades documentation on how to input long-reads (pacbio or nanopore)?