The limitations and challenges of WGS are very much the same as mentioned for WES, as they are based on the same sequencing technology [33].
Our results indicated that as low as one million reads can provide the same sequencing accuracy in transcript abundance (r = 0.99) as > 30 million reads for highly-expressed genes in all six species.
The modified pipeline (http://www.mothur.org/wiki/MiSeq_SOP) was used for the bioinformatics analysis and the number of the sequences was normalized by randomly extracting 29,966 reads to fairly compare all the samples at the same sequencing depth.
Medical oncologist Klaus Pantel of the University Medical Center Hamburg-Eppendorf in Germany, a leader in using circulating tumor cells to monitor cancer, says his group has thought about the same sequencing strategy.
The balanced strategy refers to dividing the same sequencing effort equally between cases and controls.
These increasingly noisy datasets are meant to simulate decreasing efficiency ChIP enrichments with the same sequencing coverage.
It is this information that is used to get better assembly results with the same sequencing effort.
Figure 1c shows a scenario where reads A and D have the same sequencing error at the same base.
Some of these artefacts occur within the same sequencing plate and are not reproducible when replicating the sequencing in different plates.
Previous studies using the same sequencing technology also report statistics consistent with a low level of error once the sequences have been appropriately screened for quality [7].
Secondly, the average variant frequency observed for the degradation products of EBERs detected from the same sequencing run is less than 1% across the entire 34-nt read length.
