I have deep sequencing output (thousands of reads in bam format) and I am looking for an efficient way to compute the pairwise distance (PWD) from reads with a minimum overlap
I guess it has to be a multistep approach: (1) pairwise aln; (2) compute PWD and store the resulting matrix and (3) extract the mean PWD
Would you have any advices? any existing function?
thanks in advance,