I am currently working with assembly programs and most of the assemblers output max contig length and N50. But many papers also report percent of reference genome covered by the contigs in their results. So if I have a set of contigs and a reference genome then how can I measure the percent of reference genome covered by the contigs of length greater than say x. I used NUCMER but I can get a delta or coords file as an output but not the exact percentage. Anyone knows of any tool which can output this parameter?
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The complexity of cancer is clearly demonstrated in the diverse ecosystem of the tumor microenvironment (TME). The TME is made up of numerous cell types and its development begins with the changes that happen during oncogenesis. “Genomic mutations, copy number changes, epigenetic alterations, and alternative gene expression occur to varying degrees within the affected tumor cells,” explained Andrea O’Hara, Ph.D., Strategic Technical Specialist at Azenta. “As...-
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