Details and programs for processing of the alignments are available at https://bitbucket.org/bxlab/mapper_comparisons.org/bxlab/mapper_comparisons
Our analysis suggests that primer bases should be part of read alignments and subsequent post-processing of the alignments to ensure variant calling with high sensitivity.
We analyzed the consensus reads with a standard pipeline that involves read alignment with BWA, post-processing of the alignments with GATK indel realigner, GATK base quality score recalibrator (BQSR), GATK base alignment quality (BAQ) computation [ 26], and trimming of the primer bases using custom scripts.
We propose that an effective strategy to avoid these blind spots is to incorporate the primer bases in obtaining read alignments and post-processing of the alignments, thereby effectively moving these blind spots into the primer binding regions (which are not used for variant calling).
We analyzed the simulated reads with a standard pipeline that involves read alignment with BWA [ 6, 7], post-processing of the alignments with GATK indel realigner, GATK base quality score recalibrator (BQSR), and GATK base alignment quality (BAQ) computation [ 8], trimming of the residual primer bases using custom scripts, and variant calling with GATK Unified Genotyper [ 9].
Input option set includes options for running PSI BLAST and further processing of the resulting alignment of detected homologs, such as the number of iterations, cutoff E-values, etc.
MafFilter is a command-line driven program written in C++ that enables the processing of genome alignments stored in the Multiple Alignment Format in an efficient and extensible manner.
It should be pointed out here, that though all the images shown in the results section are presented in decibels or logarithmic scale, image processing of image alignment and averaging (a few hundred images) had been done in linear scale.
The idea of our proposed method can be applied to CUDASW++ 3.0 in the future to accelerate the processing of alignments with short query sequences for the intertask kernel.
After alignment, further processing of the data was done based on the procedure laid out by Dunn, et. al. [ 23].
