![]() In addition to the primary assembly, a genome assembly may contain other sequence records, such as patches (to correct regions of the primary assembly) and/or alternative loci (to offer alternative models for highly variable regions of chromosomes). Unlocalized* and unplaced** contigs and scaffolds records may accompany the chromosome records and together constitute the primary assembly. An assembly at the chromosome level will generally have one record for each chromosome. Again, researchers represent any sequencing gaps in an assembled chromosome with NNN's. The next step is to have the scaffolds that belong to the same chromosome properly ordered, oriented, and assembled into the chromosome sequence. Assemblies at the scaffold level will generally have a number of scaffold records plus a number of contigs records. To make a scaffold a single sequence unit (a single sequence record), they represent sequencing gaps between the contigs in the scaffold with series of NNN’s (instead of DNA sequence of A, T, G, and C). To build a scaffold, researchers place several contigs in the correct order and orientation. The next step is to build scaffolds (supercontigs). This approach is termed Whole Genome Shotgun ( WGS) sequencing.Ĭontigs are the first level in the hierarchy of a genomic assembly. ![]() Once the sequences of the small pieces - called reads - are obtained, researchers assemble these like tiny pieces of a giant puzzle into progressively larger contiguous sequence pieces (called contigs). A major strategy to generate an assembly involves (1) isolation of genomic DNA from a biological sample and (2) fragmentation of DNA into small pieces that are then sequenced individually.
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