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The major obstacle has traditionally been poor or non-existent reference genomes combined with the high cost of developing oligo capture arrays required for exome sequencing, the most popular method for genotyping in humans.
In an organism with a contig-level or non-existent reference genome, selecting an enzyme with a sparse profile so each marker is covered in a large number of samples may be desirable.
Recent years have witnessed the development of a variety of statistical algorithms for haplotype reconstruction from unrelated genotype data (Stephens et al. 2001; Browning and Browning 2011; Delaneau et al. 2013) that generally rely on a pre-existent reference list of preassembled haplotypes to accurately generate phase information.
For example, one can take the argument for indispensability described above and replace all references to existent entities with references to entities assumed to exist as follows.
"He is a non-existent character.
In the case of datasets from organisms with non-existent or incomplete reference genomes, namely ones that exist as unscaffolded contigs, algorithms designed for humans fail entirely.
Whatever is non-existent remains non-existent for ever and whatever is existent always exists.
It is first of all striking in Suárez's treatment that the class of entia rationis includes a seeming motley of cases, extending beyond non-existing objects of thought and reference (and so beyond non-existent final causes).
The shelfs are referenced to an existent CAD model within a GoogleEarth/GIS framework.
Applying the so-called "nonsense formats", designed against non-existent components, to the NIBSC reference preparation of rheumatoid factor (RF), no response was found with the new assay, whereas a clear RF dose-dependent interfering signal was observed with the original assay designed for tumor tissue extracts.
(For more on reference to non-existent objects, see the entry on nonexistent objects).
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