This is a set of tools I find helpful for working with whole genome alignments stored in the SAM format. Blasr (from this repository only: https://github.com/mchaisso/blasr ), and bwa-mem may both be used to generate whole-genome alignments.

To build:

cd src && make && make install

The blasr command is:

	sawriter target_genome.fasta
blasr query_genome.fasta target_genome.fasta -alignContigs -maxAnchorGap 30000 -sam -minMapQV 30

The programs are:

• samToBed - This version of a sam <-> bed converter allows the calculation of identity
• samToDot - Create a file that may be rendered into a dotplot using RenderPlot.R
• samLiftover - Transform coordinates from the query genome to target using the SAM file as a mapping.