A Scalable GPU-Based Whole Genome Aligner, published in SC20: https://doi.ieeecomputersociety.org/10.1109/SC41405.2020.00043

a block basis estimate of the whole genome alignment estimates

stitching coding regions from exon alignments for the protein to genome alignments.

genome and transcriptome alignment extraction

formatting paf output alignments and plotting the paf alignments stats

analyzing paf alignments using awk

bactools-utility for dealing with bcf files

intergenic region analyzer from protein alignments to draft genomes.