英文內(nèi)容搬運自：
https://bioinformaticsworkbook.org/introduction/dataTerminology.html
Learning Objective
- base/nucleotide
- read
- contig
- scaffold
- chromosome
What is a base?
There are four common bases in DNA sequence, Adenine, Guanine, Cytosine and Thymine. Uracil is found in RNA in place of Thyamine
Image taken from wikipedia where more information about nucleotides can also be found.
What is a read?
A read is a string of bases represented by their one letter codes. Here is an example of a read that is 50 bases long. TTAACCTTGGTTTTGAACTTGAACACTTAGGGGATTGAAGATTCAACAACCCTAAAGCTTGGGGTAAAAC
What is a contig?
A contig is the consensus sequence generated by aligning reads to themselves.
The last line is the consensus of the aligned reads. We call this consensus sequence a contig.
What is a scaffold?
A scaffold is a set of contigs that have been ordered and oriented based on mate pair or long distance information.
contigNNNNNNNNNNNNgitnocNNNNNNNNcontigNNNNNNNNcontigNNNNgitnoc
In the line above
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contigis a string of of bases (ATC or G) - N is an unknown base
-
gitnocis the word contig written backwards to represent the reverse complement of a contig
再搜文章一些補充烤镐，有圖就更好了：
contig/scaffold 和 N50/N90
把測序的reads拼接涩咖，如果可以完全拼接起來，中間沒有g(shù)ap,則是contig.如果中間有g(shù)ap班眯，但是知道gap的長度丈秩，這樣的序列稱為scaffold.
contig N50 和scaffold N50
把contig或scaffold按照從大到小的順序排列盯捌，長度達到基因組大小（所有contig或scaffold的長度）的50%時蘑秽，那條contig/scaffold的長度饺著，即為contig/scaffold N50. N50越大，說明基因組組裝的質(zhì)量越高肠牲。同理還有N90,即達到基因組大小90%時的contig/scaffold的長度幼衰。
作者：wo_monic
鏈接：http://www.reibang.com/p/9876964e3d20
來源：簡書
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基因組組裝一般分為三個層次，contig, scaffold和chromosomes. contig表示從大規(guī)模測序得到的短讀(reads)中找到的一致性序列。組裝的第一步就是從短片段(pair-end)文庫中組裝出contig严拒。進一步基于不同長度的大片段(mate-pair)文庫扬绪，將原本孤立的contig按序前后連接，其中會調(diào)整contig方向以及contig可能會存在開口(gap,用N表示)裤唠，這一步會得到scaffolds,就相當(dāng)于supercontigs和meatacontigs。最后基于遺傳圖譜或光學(xué)圖譜將scaffold合并調(diào)整莹痢，形成染色體級別的組裝(chromosome).
https://zhuanlan.zhihu.com/p/38317398
什么是Scaffold种蘸？基因組de novo測序，通過reads拼接獲得Contigs后竞膳，往往還需要構(gòu)建454 Paired-end庫或Illumina Mate-pair庫航瞭，以獲得一定大小片段（如3Kb、6Kb坦辟、10Kb刊侯、20Kb）兩端的序列★弊撸基于這些序列滨彻，可以確定一些Contig之間的順序關(guān)系，這些先后順序已知的Contigs組成Scaffold挪蹭。Contig N50：Reads拼接后會獲得一些不同長度的Contigs.將所有的Contig長度相加,能獲得一個Contig總長度.然后將所有的Contigs按照從長到短進行排序,如獲得Contig 1,Contig 2,contig 3...………Contig 25.將Contig按照這個順序依次相加,當(dāng)相加的長度達到Contig總長度的一半時,最后一個加上的Contig長度即為Contig N50.舉例：Contig 1+Contig 2+ Contig 3 +Contig 4=Contig總長度1/2時,Contig 4的長度即為Contig N50.ContigN50可以作為基因組拼接的結(jié)果好壞的一個判斷標準亭饵。Scaffold N50：Scaffold N50與Contig N50的定義類似.Contigs拼接組裝獲得一些不同長度的Scaffolds.將所有的Scaffold長度相加,能獲得一個Scaffold總長度.然后將所有的Scaffolds按照從長到短進行排序,如獲得Scaffold 1,Scaffold 2,Scaffold 3...………Scaffold 25.將Scaffold按照這個順序依次相加,當(dāng)相加的長度達到Scaffold總長度的一半時,最后一個加上的Scaffold長度即為Scaffold N50.舉例：Scaffold 1+Scaffold 2+ Scaffold3 +Scaffold 4 +Scaffold 5=Scaffold總長度1/2時,Scaffold 5的長度即為Scaffold N50.Scaffold N50可以作為基因組拼接的結(jié)果好壞的一個判斷標準。
作者：白羊鐵蛋
鏈接：http://www.reibang.com/p/117441ac6eb8
來源：簡書
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What is a chromosome?
Chromosomes are the largest DNA molecules in a cell.
Scaffolds can be ordered and oriented using a genetic map or Hi-C data into linkage groups or chromosomes.
The ultimate goal of a genome assembly project is to assemble reads into phased chromosomes that represent an actual individual.
Most chromosomal assemblies produced today are not phased or may represent multiple individuals.
