Our group just published a paper on improving sequencing read mapping. We achieved this without inventing a new read alignment tool. The key is to customize the reference genome for each individual since mutation profile on many subjects are known a priori from previous array-based genotyping. Our software tool--RefEditor can work with any existing aligner such as BWA or bowtie.
One Size Doesn't Fit All - RefEditor: Building Personalized Diploid Reference Genome to Improve Read Mapping and Genotype Calling in Next Generation Sequencing Studies
RefEditor is freely available at
Steve
One Size Doesn't Fit All - RefEditor: Building Personalized Diploid Reference Genome to Improve Read Mapping and Genotype Calling in Next Generation Sequencing Studies
RefEditor is freely available at
Steve