A script used in conjunction with the free aligners NUCmer and the free short read assembler YASRA. Creates a file with a similar to the format to that of the .qual file YASRA outputs, except each base can have multiple sets of quality values. The format preserves all of the alignment, indel, quality, and reference data from the input files. Uses a .qual file containing the quality scores of multiple contigs and the output file of NUCmer to make a "consensus" .qual file, which contains the quality values in terms of the reference. sumqual's output can be converted to a FASTA format using qualtofa.py.
python sumqual.py [options] <.qual file>