I'm new to bioinformatics so I apologize in advance. I have a pipeline for genome assembly, the output I get is a de novo assembly file SPAdes, contigs.fasta, as well as a variant file vcf.fasta, I need to use the information about the variants from vcf.fasta and make these changes to contig.fasta, correct do I think? if yes, how can I do it better? I need to somehow combine information from vcf.fast and contigs.fast to get a consensus sequence.
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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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