Hi all,
I am trying to obtain relative abundances of assembled contigs in a number of metagenomes. My plan was to align my reads to the assemblies, calculate average coverage of each assembly, and normalize for the sequence depth of each metagenome. Unfortunately, I don't have a way of correcting for high-coverage regions in these assemblies, where it can increase by orders of magnitude and potentially skew my results. Is anyone familiar with an available tool that would help with this?
I am trying to obtain relative abundances of assembled contigs in a number of metagenomes. My plan was to align my reads to the assemblies, calculate average coverage of each assembly, and normalize for the sequence depth of each metagenome. Unfortunately, I don't have a way of correcting for high-coverage regions in these assemblies, where it can increase by orders of magnitude and potentially skew my results. Is anyone familiar with an available tool that would help with this?
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