Assembly For Rare Variants
If you detect a very rare variant using short reads (illumina) there is a good chance that it can be a sequencing error as well. Let's say I want to do some local assembly to get a better result in variant detection at this region around the detected variant. First of all, do you think this is a good idea? If so, given that there are many assemblers out there, which one do you suggest should be used for this purpose, manly based on the quality of results and ease of use for this purpose.
Thank you
1 answer
Log in to answer this question.
More posts like this
-
Method to detect CNV in a large set of coverage profile ?
written by Pierre Lindenbaum
-
Skipping The Local Realignment Around The Indels And Rather Aligning The Mapped Reads On The Exonic…
written by ivivek_ngs
-
Which Mappability Track To Use?
written by Biomed
-
Reasons Why A Region In The Human Genome May Get Bad Sequence/Alignment Using Illumina Platform?
written by Biomed
-
What Is The Best Tool To Detect Ibd In A Trio (Mom, Dad, Child)
written by Biomed
-
Detecting And Maping Balanced Translocations With Whole Genome Sequencing?
written by Biomed
-
Macrogen Vs Complete Genomics
written by Biomed
-
What Is A Good Interval For Minimum And Maximum Coverage For Next Gen Sequencing
written by Biomed
-
Any Alternatives To Penncnv?
written by Biomed
-
What Is The Best Pipeline For Human Whole Exome Sequencing?
written by Biomed
Frankly when it comes to very rare variants there are no easy to use tools. You really need to make sure to understand the entire process, to be able to make a credible statement.
I agree with you but can you be a little more specific?
The problem that you describe is quite challenging even when mapping against a known genome: http://www.broadinstitute.org/gsa/wiki/index.php/MPG_Next-Generation_DNA_sequencing_tutorials, I imagine that trying to do the same while assembling a new sequence must be even more complicated.