Let's say I have a reference genome and I sequence it into short-reads. Then, I will fed the reads to velvet to create a de novo assembly.
Let's say I have two or more contigs assembled (but not the entire genome). velvet also reports k-mer coverage for each of the contig.
For example, if AGCGGCC is my reference genome, my two assembled contigs are AG (the first two bases) and CC (the last three bases). I'm also given k-mer coverage for AG and GCC, 10.0 and 20.0 respectively.
How to find the overall coverage for the genome? In RNA, we can calculate something like RPKM abundance for a transcript but is there anything like that in metagenomics? Does my question even make sense? I know everything about my reference genome, can I report anything like coverage (or abundance) for the reference genome?
The Ray assembler gives biological abundances statistic. Is this the coverage that I'm trying to find?