De novo genome assembly is likely one of the most complex bioinformatic tasks we offer as a service. While we are promoting this as a pipeline, assembly projects more often take the form of a dialog. We typically start with a first pass attempt which we can bill as a pipeline service for a known fixed cost. From there we will start our discussions about where to go with the project.
There is no such thing as a simple assembly run. Therefore it is important to realize that, while we can often achieve very good results from a first attempt, genomes are often a never ending work in progress. A few of the issues that plague de novo assembly are: large and nested repeats, high heterozygosity leading to bubbles and miss alignments, and structural variations (large and small) between representative samples.
Our group utilizes the latest generation of long read sequencing technology and de novo assembly algorithms to provide you the most contiguous and high quality first pass assembly possible.
Potentially the most important step in producing quality long read sequencing data is the initial sample processing. The DNA sequencing center will attempt to isolate high quality high molecular weight (HMW) DNA from your organism and tissue of choice. The process is very different from traditional phenol choloform extraction, which yields quality DNA, but shears it into tiny chunks. Our HWM DNA extraction methods take steps to reduce DNA shearing, meanwhile freeing large pieces of DNA to be incorporated into libraries.
After isolating quality HMW DNA (the most difficult step), our DNA sequencing center prepares libraries for PacBio and ONT and initiates sequencing.
ORGANISMS WE HAVE ASSEMBLED GENOMES FOR:
The BRC has considerable experience assembling high quality genomes for both model and non-model organisms including:
- Dog (Canis familiaris)
- Cattle (Bos taurus)
- Hundreds of prokaryotic genomes
EXAMPLE OUTPUT REPORT:
Click the link to be redirected to our: Assembly report for sample