Genome_Coverage after assembly

pari_89

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Join Date: Apr 2013

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#1

Genome_Coverage after assembly

07-14-2013, 01:48 AM

Hi, I am probably asking a very basic question. I have assembled raw Ion Torrent reads from different tools to produce contigs. I have a reference genome, I want to know how to calculate the genome coverage from the set of contigs if that is possible.

Thank you.

Kind Regards
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kbradnam

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Join Date: May 2011

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#2

07-15-2013, 06:09 AM

One method would be to align contigs to the genome, sum the lengths of the uniquely aligned regions, and then divide that by the length of the reference genome.

Joseph Fass has some Perl/R scripts called COMPASS which will calculate this.

GitHub - jfass/compass: Perl / R scripts to COMPare a DNA sequence ASSembly to a trusted reference sequence

https://github.com/jfass/compass

Perl / R scripts to COMPare a DNA sequence ASSembly to a trusted reference sequence - GitHub - jfass/compass: Perl / R scripts to COMPare a DNA sequence ASSembly to a trusted reference sequence
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