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

intergenic region analyzer from protein alignments to draft genomes.

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

bactools-utility for dealing with bcf files

formatting paf output alignments and plotting the paf alignments stats

genome and transcriptome alignment extraction

analyzing paf alignments using awk

a ruby gem written for the protein alignments for graphs

ruby gem for analyzing miniprot protein to genome alignments.