Genome_Coverage after assembly

[pari_89]

Hi, I am probably asking a very basic question. I have assembled raw Ion Torrent reads from different tools to produce contigs. I have a reference genome, I want to know how to calculate the genome coverage from the set of contigs if that is possible.

Thank you.


Kind Regards

[kbradnam]

One method would be to align contigs to the genome, sum the lengths of the uniquely aligned regions, and then divide that by the length of the reference genome.

Joseph Fass has some Perl/R scripts called COMPASS which will calculate this.

https://github.com/jfass/compass