I have assembled bacterial genomes using SPADES. Now I am going to submit them to Genbank, but I need to know the coverage of each assembly. Should I provide the raw read coverage or the filtered final coverage? If the second possibility is true, how do I access these values from the SPADES log file?
The best way to calculate coverage is by mapping, not by looking at the assembler's logs. For example, with BBMap:

    bbmap.sh in=reads.fq ref=contigs.fa covstats=covstats.txt

That will print a message like this:

```
Average coverage:                       278.50
Percent scaffolds with any coverage:    100.00
Percent of reference bases covered:     99.98
```

...in addition to creating `covstats.txt` which will list the coverage statistics for each individual scaffold. The reads you use for mapping should be the ones you fed into Spades.