What does exactly the contig coverage mean?

[SDPA_Pet]

Can anyone give the definition about "contig coverage" mean? I am confused about it? Does it mean the number of reads used to assembled to this particular contig?

I also hear coverage? When you do illumina sequencing. What does coverage in sequencing mean? How can you calculate it?

Do these two coverage use the same calculation method?

Thanks.

[jmartin]

Its usually best if you can ask the person providing that value what exactly they mean if you aren't sure since there are a number of legitimate ways people use the word 'coverage'.

My naive assumption when someone says 'contig coverage' is that they are talking about the average number of reads spanning each given base position. This value would have been calculated by taking the total no. of bases that map to the contig divided by the contig length. And if the value is an average across many contigs, then its taking the total no. of bases mapping to all contigs divided by the total length of all contigs.

I think when someone is talking about a request for illumina sequencing, and they talk about wanting '200x' coverage worth of illumina sequencing, in that context they are talking about the total number of bases of sequencing they will produce divided by the estimated length of the genome. This coverage value is much more of an estimate than one based on actual mapping (or the internal knowledge of how many reads span each position that an assembler may report as a post-assembly metric). So a request for 100x illumina coverage of a 50Mb genome means you want enough illumina runs to generate 5000Mb of illumina read data. This coverage value can often differ from what you find after you actually assemble the data. If your genome size estimate was wrong, or of the assembly is bad, you may find that the actual 'coverage' you have of the genome will be different from your initial estimate.

I am making a lot of assumptions here, but these would be my guess at what people mean when they are talking about the coverages you are asking about.

[SDPA_Pet]

Hi Jmartin,

Thanks. I think the contig coverage explanation is what I need.

For the sequencing coverage, your example is for a genome. I am doing environmental metagenome. So, the sequencing coverage doesn't apply for my case, because I don't have the prior knowledge about my metageome. I don't know how large it is.

[jmartin]

Hmm, yeah I wouldn't know what exactly someone meant by 'illumina coverage' for a metagenomic sample. Unless you already know the community makeup and know the genome sizes. And even then the composition of the community would make it tricky since some genomes may be present in abundance and others may be rare.

Sorry, hopefully someone more in the know will reply.