Question: Hybrid assembly with MiSeq and PacBio reads in ABySS
gravatar for steven
5.6 years ago by
United States
steven70 wrote:

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.

assembly • 2.5k views
ADD COMMENTlink modified 5.6 years ago by h.mon32k • written 5.6 years ago by steven70
gravatar for h.mon
5.6 years ago by
h.mon32k wrote:

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.

ADD COMMENTlink written 5.6 years ago by h.mon32k
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