This figure shows the alignment process on one 3D object of the gallery set.
We re-aligned our positive sample using TopHat (Trapnell et al., 2009b), which considers splice junctions in the alignment process, to test the confounding effect of splice junctions presence on our results.
The generated pseudogenome is then used in the alignment process instead of the reference genome, so the end result of alignment is a BAM file (14) using the coordinate system of the pseudogenome.
It is important to note however, that reference bias is an artifact of the alignment process, rather than of the data, and can be greatly reduced by locally realigning the reads based on the reference and the data.
The aligned fraction of CNTs serves as an important parameter for the quality control of the alignment process and numerical simulations of structure property relationships of CNTNs and their composites.
Although the running times of BFAST are slower in the majority of cases compared to other methods, when considering the need for sensitivity and accuracy of the alignment process in the context of whole-genome resequencing (see simulations above), BFAST has attractive advantages including the ability to be implemented in a parallel computational environment.
The computing time of the alignment process depends on the size of the input networks.
The covariation in the misaligned region can not be due to shared ancestry, but rather is an entirely synthetic side-effect of the alignment process and thus the phylogeny correction of Zp does not compensate for it.
The unbiased alignment process of MSARC may simplify this procedure and improve the reconstruction accuracy, especially in the most problematic cases.
Therefore, we can significantly reduce the computational complexity of the alignment process by inserting seeds only into a limited number of query positions that are likely to be extended.
