什么是Scaffold?


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红橙子

基因组de novo测序,通过reads拼接获得Contigs后,再通过大片段文库(如3Kb、6Kb、10Kb、20Kb)两端的序列。来确定一些Contig之间的顺序关系,这些先后顺序已知的Contigs组成Scaffold。

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omicsgene - 生物信息
擅长:重测序,遗传进化,转录组,GWAS

A contig is a contiguous length of genomic sequence.
A scaffold is composed of contigs and gaps. Gap length can be guessed by incorporating information from paired ends or mate pairs

What is a Scaffold?

A scaffold is a portion of the genome sequence reconstructed from end-sequenced whole-genome shotgun clones. Scaffolds are composed of contigs and gaps. A contig is a contiguous length of genomic sequence in which the order of bases is known to a high confidence level. Gaps occur where reads from the two sequenced ends of at least one fragment overlap with other reads in two different contigs (as long as the arrangement is otherwise consistent with the contigs being adjacent). Since the lengths of the fragments are roughly known, the number of bases between contigs can be estimated.

attachments-2018-09-4rbXQeJS5ba2fd376aad3.jpg

The goal of whole-genome shotgun assembly is to represent each genomic sequence in one scaffold; however, this is not always possible. One chromosome may be represented by many scaffolds (e.g., Chlamydomonas reinhardtii) or just a single scaffold (e.g., Human chromosome 19), depending on how completely the genome can be reconstructed, or assembled, from the available reads.  The relative locations of scaffolds in the genome are unknown.

Scaffolds are normally numbered approximately from largest to smallest. Some scaffolds may ultimately be filtered out of the assembly, resulting in skipped scaffold numbers.

In some cases, scaffolds can overlap. For example, in polymorphic genomes, regions with a high density of allelic differences between haplotypes may be split into separate sets of scaffolds, each representing one allele. Thus, a sequence that exists in only one location in the genome may appear on more than one scaffold.

Gaps are shown in the Genome Viewer as red lines or rectangles in the scaffold track (viewed in "full" mode). Contigs are shown in black. In FASTA sequences, gaps are represented by a series of Ns.

 

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  • 红橙子 提出于 2018-09-19 23:07

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