coverage plot

[golharam]

IGV does a great job of displaying coverage information, but you do need to zoom in enough. I want something more on the chromosome level to get an overview of my coverage.

Thank you for all the suggestions. I'll have to spend some time looking at these.

[bioinfosm]

Maybe the alignment view of IGV is enough for want you want, it has a coverage track:

http://www.broadinstitute.org/igv/AlignmentData

For a completely different idea you could also have a look at (the R package for) Hilbert curves:
http://www.ebi.ac.uk/huber-srv/hilbert/

I think IGV has the issue of displaying alignment only if you zoom-in enough.. not sure if that is true for the coverage track as well!

[ulz_peter]

Savant can do that as well. If've got a BAM file of your aligments you can convert it into a BAM Coverage files. That allows you to display coverage along a chromosome easily. I attached a picture of a whole human chromosome 1 coverage plot.

Hope that helps,
Best regards,
Peter

[simonandrews]

One of the features for the next release of SeqMonk will be a whole genome view. This will display the current quantitation for a single sample over the whole genome so you can configure it to show pretty much anything you want.

[maubp]

I've done coverage plots of small (circular) genomes using Biopython and GenomeDiagram, things like mitochondria or viruses - should work fine for bacteria too. However, this isn't an off the shelf point and click solution.

[svl]

Maybe the alignment view of IGV is enough for want you want, it has a coverage track:

http://www.broadinstitute.org/igv/AlignmentData

For a completely different idea you could also have a look at (the R package for) Hilbert curves:

http://www.ebi.ac.uk/huber-srv/hilbert/

[golharam]

to start with, the length of the chromosome and the coverage information, perhaps in wig format.

For fancier stuff, say customizing color, size of the image (in pixels), how the +/- strand information is displayed, etc.

[ECO]

What's your desired input format for the script?

[golharam]

Can anyone recommend a good tool to display a coverage plot over a chromosome? The images produced by UCSC aren't of great quality nor can I customize it. I'm curious what most people use to generate high quality coverage plots with.