Removed contigs and genes from assembly by HaploMerger

Question

[Mehmet]

I used HaploMerger, now I want to see which contigs and genes were removed from assembly by HaploMerger. How can I do that?

Thanks

Answer 1

[thackl]

One way to go would by alignment of the old and new assembly. A very fast way is probably bwa mem - viewing the resulting BAM file in IGV or similar is also straight forward. A more sophisticated way would be using mummer/nucmer, the results can be visualized as dotplots as well.

Answer 2

[mapleforest]

You can try HaploMerger2, the newly-upgraded package.