Today I had a little assembly course. They showed us the closed source SW "SeqMan Pro".
In this SW you have a nice mode, where you can load contigs individually and then see how two Illumina paired end reads map to other contigs, if they span the ends (so you have a closed contig), etc...
If there a nice open source SW to do that visually?
Couldn't you use the Integrative Genome viewer (IGV)?
You can just index your assembly (or whatever it is that has your contigs). Then load that assembly as a "genome" (doesn't matter if it is not an actual reference genome).
Once it has loaded, just load the sam/bam file which holds the alignment data for the PE reads.
Select the contig you want to see from the drop-down bar on the top or type it in... and you should have the contig and the reads that were aligned to it in one window. You can then just zoom in etc to see the individual bases etc
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Sounds good! I will try that!