Question: How to measure NGS depth coverage bias
gravatar for Anand Rao
6 months ago by
Anand Rao110
United States
Anand Rao110 wrote:

Is there a software tool that reports a measure of the degree of non-uniformity in depth of Illumina sequencing coverage across a de novo assembled genome (against which the Illumina reads are mapped back)?

I have the PE read library (2150bp HiSeq4000), the *de novo assembled genome, and the BAM file for mapping of former to the latter - and I have 290 such data points. I am curious to know how many of these 290 have more versus less uniform coverage depth across their respective genomes.

I came across a paper -, but no software tool name per se. Some of my assembly woes may mirror those from an earlier post at Any advice for a de novo genome assembly .

To reiterate: Is there a software (like a supplement to something like BBTool's bbnorm) that can help visualize quickly which of my genome assemblies are built on the basis of more uniform coverage depth?

ADD COMMENTlink modified 6 months ago by Len Trigg1.1k • written 6 months ago by Anand Rao110
gravatar for Len Trigg
6 months ago by
Len Trigg1.1k
New Zealand
Len Trigg1.1k wrote:

One measure of non-uniformity of coverage is the fold-80 penalty, (see Essentially it is the degree of additional coverage (in fold coverage of the genome) required so that 80% of the target bases will be covered at the current mean coverage.

The rtg coverage command from RTG Core computes the fold-80 penalty, in addition to other statistics and graphs that can be used to visualize coverage distribution information.

ADD COMMENTlink written 6 months ago by Len Trigg1.1k
gravatar for Brian Bushnell
6 months ago by
Walnut Creek, USA
Brian Bushnell15k wrote:

If you map reads to an assembly, you can use BBMap's like this: in=mapped.sam stats=covstats.txt hist=hist.txt

From the histogram you can visualize the uniformity of the coverage. stats.txt will contain the average coverage and standard deviation on a per-scaffold basis. The program will also print to the screen the overall average coverage and standard deviation.

ADD COMMENTlink modified 6 months ago • written 6 months ago by Brian Bushnell15k

You've got


flag twice, so could you have meant out=covstats.txt?

ADD REPLYlink written 6 months ago by Anand Rao110

Fixed, thanks :) It actually doesn't matter (the second stats= overrides the first one). For, covstats, stats, and out are synonymous...

ADD REPLYlink written 6 months ago by Brian Bushnell15k
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