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Removed contigs and genes from assembly by HaploMerger

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

Thanks

genome gene sequencing assembly alignment
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updated by mapleforest • mapleforest • written by Mehmet Mehmet

2 answers

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.

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written by thackl thackl

You can try HaploMerger2, the newly-upgraded package.

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written by mapleforest • mapleforest

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