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.