# 末端接头剪切（adapter trimming）时需要用到的序列
在illumina测序仪上进行测序时，如果测序读长大于插入片段长度，那么文库3’端接头(adapter)序列会出现在FASTQ文件 [3’ 末端](https://support.illumina.com/bulletins/2016/04/adapter-trimming-why-are-adapter-sequences-trimmed-from-only-the--ends-of-reads.html) 。为了防止这段接头序列对下游比对产生影响，可以在比对前将3’末端的接头序列去除（adapter trimming）。这项功能在FASTQ生成的流程中是可选项。利用[Illumina Experiment Manager](http://support.illumina.com/sequencing/sequencing_software/experiment_manager.html) IEM编写的SampleSheets，在\[Settings]部分包含了针对illumina建库试剂盒的接头序列，BaseSpace Sequence Hub Prep, BaseSpace Sequence Hub Instrument Run Setup及 Local Run Manager 已经整合并包含了illumina建库试剂盒中所带有的接头序列，但是一些第三方数据分析软件则需要单独指定末端接头剪切所需的序列。每种illumina试剂盒推荐的末端接头剪切的序列如下：
备注：若下方只列出了一条序列，则代表双端测序Read1和Read2使用的接头序列相同，均为列出的这一条序列。若双端测序中Read1和Read2所用的序列不同，则两端对应的接头序列均会列出。
TruSeq single index (更名前的LT) and TruSeq CD index (更名前的HT)-based kits:
· Read 1: AGATCGGAAGAGCACACGTCTGAACTCCAGTCA
· Read 2: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT
AmpliSeq for Illumina; Illumina DNA Prep (M) Tagmentation (更名前的 Nextera DNA Flex); Illumina DNA Prep with Enrichment (S) Tagmentation (更名前的 Nextera Flex for Enrichment); Nextera DNA; Nextera XT; Nextera Enrichment; Nextera Rapid Capture Enrichment; TruSight Enrichment; TruSight Rapid Capture Enrichment; TruSight HLA; Illumina Stranded mRNA Prep, Ligation; Illumina Stranded Total RNA Prep, Ligation with Ribo-Zero Plus; Illumina RNA Prep with Enrichment, Ligation
· CTGTCTCTTATACACATCT
Illumina DNA PCR-Free Prep, Tagmentation
· CTGTCTCTTATACACATCT+ATGTGTATAAGAGACA
Illumina Stranded mRNA Prep, Ligation and Illumina Stranded Total RNA Prep Ligation with Ribo-Zero Plus:
* ACTGTCTCTTATACACATCT
ScriptSeq and TruSeq DNA Methylation:
· Read 1: AGATCGGAAGAGCACACGTCTGAAC
· Read 2: AGATCGGAAGAGCGTCGTGTAGGGA
TruSeq Small RNA:
· TGGAATTCTCGGGTGCCAAGG
Nextera Mate Pair:
· CTGTCTCTTATACACATCT+AGATGTGTATAAGAGACAG
备注：
· 如果使用illumina的专有分析流程，针对TruSeq Targeted RNA Expression，TruSeq Custom Amplicon及TruSeq Cancer Panel的文库不需要做末端接头剪切。另外，享有专利技术的TruSeq Synthetic Long-Read文库在[组装](https://basespace.illumina.com/apps/551551/TruSeq-Long-Read-Assembly)会自动去掉接头序列。
· 关于Nextera Mate Pair文库的末端接头剪切，更多信息请参见[Data Processing of Nextera Mate Pair Reads on Illumina Sequencing Platforms](http://support.illumina.com/content/dam/illumina-marketing/documents/products/technotes/technote_nextera_matepair_data_processing.pdf) 技术小贴士。
· 不同的illumina文库制备试剂盒的全部接头序列信息可以在[Illumina Adapter Sequences Document](https://support.illumina.com/downloads/illumina-adapter-sequences-document-1000000002694.html)中找到。
· 对于Illumina Stranded mRNA Prep, Ligation 和 Illumina Stranded Total RNA Prep Ligation with Ribo-Zero Plus文库，需要将文库5’端突出的一个T碱基去除。详细内容请参见"[Trimming T-overhang options for the Illumina Stranded mRNA and Illumina Stranded Total RNA workflows](https://support.illumina.com/bulletins/2020/06/trimming-t-overhang-options-for-the-illumina-rna-library-prep-wo.html)" 小贴士。
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| *For any feedback or questions regarding this article (Illumina Knowledge Article #7122), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000007122%20-%20Library%20Preparation%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* |
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