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.