What happen if the sequenced reads don't distribute uniformly across the genome? What is the resulting effect for variation detection? Is there any qualitative research on this?I see many papers writing that "assume the reads are sampled randomly from the sample genome", but if it is not equally distributed, what will the result be?
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Hi, I am dealing with similar problems.. I am reading through this special edition, which might be useful..
I know that some assemblers (e.g. MIRA3 with uniform_read_distribution switch) have settings to not assume that read distribution is uniform. These seem to be mainly used for EST sequencing assembly but would also be relevant for exome sequencing. What effect that has, I don't know. I would assume that low coverage regions would be problematic: this paper (http://www.ncbi.nlm.nih.gov/pubmed/20980557) suggests that low coverage regions caused by heterogeneous coverage result in a high rate of false positive SNPs. Any experts want to help?
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Researchers using sequencing and genomics tools often have to make trade-offs. They can choose between speed or scale, short reads or long-range information, or targeted panels or a view of the whole transcriptome. New technologies that have been released this year are built to address those tough choices.
We asked six companies the same four questions to learn about their latest products. The new technologies bring a lot to the table, including rethinking sequencing...
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