Question: Hybrid assembly with MiSeq and PacBio reads in ABySS
1
gravatar for steven
3.7 years ago by
steven70
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 • 2.0k views
ADD COMMENTlink modified 3.7 years ago by h.mon24k • written 3.7 years ago by steven70
2
gravatar for h.mon
3.7 years ago by
h.mon24k
Brazil
h.mon24k 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 3.7 years ago by h.mon24k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1267 users visited in the last hour