[mira_talk] Re: Making the best assembly

  • From: C Jenkins <cej.jenkins@xxxxxxxxx>
  • To: mira_talk@xxxxxxxxxxxxx
  • Date: Sun, 6 Dec 2015 20:19:09 -0800

That's one of the problems, this is the first data we have for this
parasite. We don't really know the average genome size, the chromosome
number or how many contigs we really should have. I said "significantly
fewer contigs than expected" because we compare it to Schistosoma, which
has 13,000 contigs. So 530.... is significantly less than that.

I have cDNA library from an mRNA isolation, so only transcribed sequences.
I do have access to a large terabyte single node.

I was under the impression that MIRA would be good at hybrid assemblies?

On Sun, Dec 6, 2015 at 8:04 PM, Rick White <raw937@xxxxxxxxx> wrote:

What type if data do you have? RNA or DNA? Avg genome size? Chromosome
number? I am close to you if you need help. I am in PNNL in central
washington. Do you have access to a large terabyte single node? You can try
minimus2 to merge assemblies.

Cheers
Rick
On Dec 6, 2015 8:00 PM, "C Jenkins" <cej.jenkins@xxxxxxxxx> wrote:

I have a largely undescribed species of a trematode parasite. It is
similar in life cycle to Schistosoma mansoni.

I have 454 and illumina single end reads from 4 different populations. I
need to first create a reference transcriptome.

The illumina data is... rough. I first assembled it using Trinity, and
found only 531 contigs... which is orders of magnitude less than I
expected.

So I used MIRA to do a 454 assembly, a illumina assembly and a hybrid
assembly. Now I'm trying to figure out which is any good.

MIRA Assembly Statistics

Platform

Reads

# Contigs

Max

Coverage

Average Quality

454

33779

1938

43505

45

Illumina

72276

3033

34767

43

Hybrid

454 and Illumina

98259

6726

77610

55


Obviously there are the most contigs in the hybrid assembly, but the
percentage of reads from each population that map to the reference is
significantly lower (~55% of reads from each population map to the
reference).

How could I improve this? I'm drowning a bit in the literature and
any/all help is welcome.

Thanks!

CJ
--
CJenkins, MS
PhD Candidate
Washington State University/University of Idaho




--
CJenkins, MS
PhD Candidate
Washington State University/University of Idaho

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