through analyzing the wgs of bacterial strain on the galaxy platform, I faced one problem, how can I calculate the genome coverage (depth) using galaxy tools. I spent a long time trying to figure out the best way to do so. As I understood, we can calculate it manually as C=L*N/G, where L= read length, N number of reads, and G genome size. However, I am still missing few points:
1- Is read length the same for all reads as for example 151 in my case
2- Just to be sure, N of reads should be after trimming adapters and <20 bp reads (correct me please)
3- genome size = the total length of the assembly contigs (correct me please)
4- Is there any tool that can show the totals length of the reads after trimming using Trim-galore (since this tool statistics show the N of reads and the length is written as (20-151)
Many thanks for your help, and sorry for such a long q.