There are already a number of tools already available for reference-free SNP calling (see Table 1).
Although qNMR reference standards are already available as certified reference materials (CRM) providing traceability on the basis of H qNMR experiments, there is an increasing demand for purity assays on phosphorylated organic compounds and metabolites requiring CRM for quantification by P qNMR.
These extracted unmapped mate reads were then mapped to the F. graminearum reference genome, already available for the strain PH-1, resulting in two stacks of reads for each plasmid sequence insertion.
Moreover, to facilitate simultaneous annotation of one or several genomes for which a closely related species considered as a reference genome is already available, an ideal strategy would include two steps: first, an update of the reference genome annotation, and second, the annotation of the new genomes based on the re-annotated one.
First, though, why would anyone need an app when nearly every bit of reference material is already available from a mobile browser?
Quantitative trait locus (QTL) mapping is a powerful approach to identify key genomic regions controlling adaptive traits [ 3, 24, 25], especially for species where a reference genome is already available [ 26].
The enrichment of DNA target sequences was validated by real-time PCR, whereas the efficacy of the applied strategy was evaluated by mapping the 454-output reads against reference transcript data already available for M. galloprovincialis and by measuring coverage, SNPs, number of de novo sequenced introns, and complete gene sequences.
Due to their relevance for the oral route of exposure, different silicon dioxide (SiO2) and zirconium dioxide (ZrO2) NMs were selected for the oral toxicity studies, and they were compared to nanoparticular barium sulfate (BaSO4), for which extensive physico-chemical information is already available since it is the OECD reference nanomaterial NM-220 (OECD 2008a; Hellack et al. 2012).
For genera where a reference genome is already available [ 1] or for others with large and unsequenced genomes such as for the vast majority of forest tree species, quantitative trait locus (QTL) mapping still represent an attractive approach that can help improve our comprehension of the genomic architecture of adaptive traits [ 2- 4].
This procedure is shown in Figure 5, where the quadrilateral in frame X b is warped to a square block in the current frame X f (left square block), where a reference square block (right block) is already available.
