visualization of PE/MP reads connection on assembly

Question

[yifangt86]

Hello,

I am looking for open source tools/script to visualize the PE/MP reads connections on assembled contigs/scaffolds. IGV or Tablet show the the abundance along the template, but I am looking for the connections of the pairs showing the relative distance in between. Here is an example, but the author did not respond.

Thanks a lot!

[h.mon]

Where, in this 192 (!!) pages supplement, is the figure you want to highlight? Anyway, did you have a look at Bandage? Maybe is the kind of tool you want.

[Prakki Rama]

Map the reads separately and get two bam files. Load them as two tracks in IGV. You should be able to visualize simultaneously.