With the launch ofAmpliSeq for Illuminaproducts, DNA Amplicon and RNA Amplicon analysis modules for本地运行经理2have been released.

• 本地运行管理器2可用于ISEQ，MiniSeQ，Miseq和NextSeq 500/550系统的数据的缺消仪器分析，以及运行Miseq控制软件版本3的ISEQ和Miseqs的板载。
• For instruments without on-instrument Local Run Manager 2, analysis must be performed using an off-instrument installation.
• 对于MiniSeQ用户，请参阅如何设置一个AmpliSeq最佳a run using Local Run Manager for MiniSeq bulletin.

After sequencing has finished, transfer the complete run folder to a computer where off-instrument Local Run Manager 2 with AmpliSeq modules is installed.Note:Run data must be copied to the local computer. Local Run Manager may fail to import runs from locations in user-specific folders, such as Desktop and Documents. Analysis of run data from a network location is not recommended. Users performing DNA Amplicon analysis must also download and install the version of the hg19 human genome available on the本地运行管理器支持网站。

To analyze data with Local Run Manager 2 off-instrument, first create the run either manually or by importing a sample sheet:

Option 1, manual run setup:

1. Select创建运行from the Local Run Manager dashboard and select either DNA Amplicon or RNA Amplicon.
2. 输入Run Name并选择AmpliSeq Library PLUS for Illumina(96) from the Library Kit dropdown menu.
3. 选择分析所需的特定模块特定设置。有关更多信息，请参阅DNA AmpliconandRNA扩增子analysis module guides.
   • When performing DNA Amplicon analysis, AmpliSeq for Illumina libraries are aligned using theBWA Whole-Genomealigner. The TruSeq Amplicon aligner is for TruSeq Amplicon libraries only.
   • indel重新调整是可选的设置。使用此选项可以改善介质诱导的检测，但对整体精度的变化可能取决于特定面板。选择Indel Realignment选项时，总分析时间将增加。如果您想打开此选项：
     1. 展开显示高级模块设置
        
     2. Select + Add custom setting
        
     3. EnterVariantCallerRealignIndelsin the field “Type custom setting here”
     4. enter1for true in the field “Type setting value here” to enable the Indel realignment option.
        
4. Enter Sample IDs in the sample table and choose the index plate well from the dropdown menu. The contents of each well can be found in the索引适配器池指南。在dex sequences will populate automatically.
5. 进口or select the manifest from the Manifest dropdown menu and select the reference genome from Genome dropdown menu.
6. Select保存运行返回本地运行管理器仪表板或出口样品表保存运行配置的副本以备将来使用。

Option 2, set up with sample sheet:

1. Sample sheets can be created usingIllumina Experiment Manager1。15 or later or using Local Run Manager. When using Illumina Experiment Manager, selectMiSeqas the instrument andFASTQ Onlyas the application.
   • Note:Local Run Manager will automatically reverse complement the second index when performing analysis of MiniSeq and NextSeq 500/550 data. The forward (MiSeq) orientation of indexes should always be used.
2. Select创建运行from the Local Run Manager dashboard.
3. 从下拉菜单选择DNA AmpliconorRNA扩增子from the Local Run Manager dashboard.
4. Select进口Sample Sheet。
   
5. 如果在样本表中未指定实验名称，则输入RUN名称。
6. Follow steps 3-5 of option 1 to choose module-specific settings, the manifest, and the reference genome.
7. Select保存运行返回本地运行管理器仪表板或出口样品表保存运行配置的副本以备将来使用。

运行现在将显示为Ready进行排序。要开始分析：

1. Select更多选择(the three grey dots on the right of the run name) and select进口。
2. 在进口Run窗口，输入运行文件夹位置的路径。
3. 输入将保存分析结果的输出文件夹的位置。输出可以是使用完整UNC路径的本地驱动器或网络位置。映射的字母驱动器不支持网络输出位置。
4. Select进口Run。The analysis will start automatically.