In order to minimize false SV calls supported by the assembly, the assembled contigs were aligned to the reference human genome using an additional alignment algorithm SSAHA2 [ 34], and the SVs again validated using R-SAP.
Upon every BLAST search, an additional 'Alignment Track' labeled "BLAST" gets added in the Browser for users to see the exact region of the genome aligned to the query, without any requirement for manual intervention.
For an additional alignment, a post-processing toolset (Picard; http://broadinstitute.github.io/picard/) was then used to perform local realignment, duplicate marking, and score recalibration to generate a final aligned set of genomic reads.
We computed an additional alignment of the HIV-1 and SIVcpz viruses only (HIV-1/SIVcpz alignment).
We also added an additional alignment, which includes other atypical kinases as Figure 2 figure supplement 1.
While a second, allele-aware alignment increases accuracy at predicted heterozygous sites, these modest gains, still accompanied by a high rate of false discovery, require an additional alignment.
Fully valid reporters are permitted to have additional alignments to their corresponding gene, to the reverse complement of a different gene, to intergenic regions, or to untranscribed pseudogenes.
An additional alignment related effect is tilting of the retina in axial direction.
Specifically, BWA-aligned genomes were subjected to an additional local alignment within GATK to improve the accuracy of SNP calling by locally realigning areas where there might be insertions or deletions (McKenna et al. 2010).
Additional alignment algorithms were used to define transcript-specific probe sets employing different databases as RefSeq or AceView [6], [7].
