Questions tagged [scaffold]

A set of contigs, the order of which corresponds to consecutive genomic locations. Contigs can be scaffolded using a reference genome or optical mapping.

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Is it possible to determine the genomic context of a gene in a Whole Genome Shotgun project?

I performed several BLAST searches and identified several genes of interest in a Whole Genome Shotgun (wgs) project. I know that gene X is located on scaffold 1234, from nucleotide 1 - 2250, while ...
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How to extract homologous sequence data from multiple .vcf.gz files?

I have short read data from multiple samples stored as scaffolds.vcf.gz files. I have some gene sequence of interest. I want to find the closest homologous sequence ...
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Resources to learn genome assembly workflow for small genomes (like viruses)

I have sequencing data of a few samples of a DNA virus. I'd like to learn de novo assembly of 'short read' data, to construct a scaffold and then count the abundance of each strain in the data. I ...
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