I have genomic reads from PacBio and Nanopore. I also have a few Illumina RNA-seq runs for this organism.
Is it possible to use ALL of these to generate a consensus assembly?
I know there is Hybrid-SPAdes but I don't know if you can give it both PacBio and Nanopore... plus, I don't think it wants RNA-seq reads.
2 answers
I know at least Canu can use PacBio and NanoPore reads simultaneously to assemble a genome - there may be other assemblers out there capable of mixing PabBio and NanoPore input data.
After assembly, you may use Pilon with the RNAseq data to polish the draft assembly, see Using pilon with RNAseq data #50, Racon may also work.
Do you know if Hybrid SPAdes is design to take in RNA-seq data as well as the long read genomic data?
No, not together with shotgun genomic sequencing.
Also, can it take both PacBio and Nanopore?
Yes. From the manual:
To run SPAdes 3.12.0 you need at least one library of the following types: Illumina paired-end/high-quality mate-pairs/unpaired reads IonTorrent paired-end/high-quality mate-pairs/unpaired reads PacBio CCS reads Illumina and IonTorrent libraries should not be assembled together. All other types of input data are compatible. SPAdes should not be used if only PacBio CLR, Oxford Nanopore, Sanger reads or additional contigs are available.
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Genome or transcriptome assembly? You can't mix whole genome DNAseq and RNAseq for genome (or transcriptome) assembly, but you can use the RNAseq for scaffolding after genome assembly.
You may also use the Illumina RNAseq for polishing the Pacbio / NanoPore genome assembly.
The SPAdes manual imply you can use both simultaneously. Why don't you try and find out?
Yes, that is the terminology I was looking for with polishing my scaffolds with RNA-seq (thanks)! My goal is to have a polished genome assembly (not transcriptome assembly). I was under the impression that Hybrid-SPAdes wants shotgun genomic reads with long reads?
How much coverage on the Longer reads are you looking at? Also how much data do you have from RNASeq?
It might just be easier to assemble the longer reads together and then use the RNASeq data to scaffold.