i would like to relate the coverage of a contig, resulted from a NGS sequencing, to its length and relate this value to the genome length for comparing quality of contigs for different assemblies and in the end the quality of each assembly in genera.
for a genome 150kb in legth there are 3 different genotypes sequenced (lets call them a,b,c), each one with a set of contigs.
contig1a: coverage 1000x and length 50kb
could be much more useful than
contig1b: coverage 200x and length 50kb
contig1c: coverage1000x and length 1kb
where contig1a, contig1b, contig1c belong to 3 different genotypes and so to different assemblies.
i know the parameter NG50 but i want to relate this parameter to the coverage and set a quality value for each contig, which for me is very important.
Anyone can help?
Thanks in advance