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For a variety of reasons, cross-platform alignment occurs too infrequently.
SeaView (Galtier et al., 1996) is a specialized cross-platform alignment editor developed for molecular phylogeny studies.
The key features of AliView include the ability to swiftly handle large alignments with low memory impact (see Table 1 for comparison with other popular free cross-platform alignment viewers).
In Phase I of the 1000 Genomes Project, genotypes were called using a combination of different approaches: first, primary call sets were independently generated by different centers with different sequencing platforms, alignment, and variant calling methods; then, a consensus SNP call set was generated and made publicly available (The 1000 Genomes Project Consortium 2012).
This work represents a critical step in communications for networking of heterogeneous unmanned systems and establishes a solid platform for alignment of development and ongoing programs.
We have also set-up platform-specific alignment protocols.
In addition, due to the intrinsic biases from sequencing platforms, the alignment differences might reflect some inevitable sequencing errors.
The discrepancy mainly results from other factors such as characters intrinsic in sequencing platforms, read alignment and variant calling methods.
It is known that different NGS platforms and alignment tools have biases that can introduce false positives [ 37– 40].
Sequencing platforms and alignments.
To evaluate the accuracy of a base call in each platform after the alignment procedure, we used the "conservation" score, generally used in relationship to alignments of sequences originating from different species.
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