Hybrid assembly with MiSeq and PacBio reads in ABySS

Question

[steven]

I have a set of paired end and single end MiSeq Illumina reads: Sample_1.fastq, Sample_2.fastq, Sample_s.fastq

If I wanted to assemble this with Abyss it would be:

abyss-pe K=Kmer name=Sample_Kmer in='Sample_1.fastq Sample_2.fastq' se='Sample_s.fastq'

Now I want to perform a hybrid assembly with pacbio reads thrown into the mix. I have 3 PacBio subreads: Sample.1.subreads.fastq, Sample.2.subreads.fastq, Sample.3.subreads.fastq (all ~2 gigabytes)

My question is, how do I include all of these read files in one assembly command?

I was able to do this in Spades/Soapdenovo so far.

Answer 1

[h.mon]

I think Abyss will not use long reads on the assembly step, it will only use long reads for scaffolding - check on its manual. Cerulean performs hybrid assembly starting from an Abyss assembly, but it is designed for small genomes.