NGS Read Alignment Advising
Using our previous experience with parameter advising on existing bioinformatics tools, we are currently working with a set of NGS aligners to make input-specific parameter choices for this problem.
Advances on this topic would improve downstream analysis on many fronts, including out previously studied work on transcript assembly.
Structure-Aware Protein Multiple Sequence Alignment Advising
The beta version of the Opal alignment tool (opal.cs.arizona.edu, GitHub: github.com/deblasiolab/Opalv3) allows for the inclusion of predicted protein secondary structure when constructing multiple sequence alignments. This extension was not included in our initial study of the impact of parameter advising on alignment.