Illumina Preset Protocol - Nextera DNA Flex

Workflow 1 : Nextera DNA Flex for Small Genomes

• Protocol 1: Nextera DNA Flex DNA Quantification
• Protocol 2: Nextera DNA Flex Library Prep for Small Genomes

The library prep kit includes the following 4 workflows based on the input DNA:

• Workflow 1 for DNA between 1-100 ng
• Workflow 2 for DNA >100ng
• Workflow 3 for Blood samples
• Workflow 4 for Saliva samples

Workflow 2: Nextera DNA Flex for Large Complex Genomes

• Protocol 1: Nextera DNA Flex Library Prep for Large Complex Genomes

Workflow 3: Nextera DNA Flex for Blood Samples

• Protocol 1: Nextera DNA Flex Blood Lysis
• Protocol 2: Nextera DNA Flex Library Prep for Blood Samples

Workflow 4: Nextera DNA Flex for Saliva Samples

• Protocol 1: Nextera DNA Flex Saliva Lysis
• Protocol 2: Nextera DNA Flex Library Prep for Saliva Samples

Alternative step if combining all options.

Master Step 1: Tagment

Process Type 1: Tagment Genomic DNA (Nextera DNA Flex)

Input = DNA

Output = Tagmented DNA

SharedResultFile = Log File

Reagent Kits

Kit Name

Supplier

Nextera DNA Flex Library Prep Kit, Box 2 (20018704/20018705) TB1

  

Nextera DNA Flex Library Prep Kit, Box 3 (20018704/20018705) BLT

  
Record Details

Section

Subsection

Setting

Value

Specification

Step Data

Multiline Text Fields

Comment

Multiline Text

  

Step File Placeholders

 

File Name

Log

Auto

Sample Table

Table Columns

Desired DNA Amount (ng)

Text

  
   

Nuclease-free water (µl)

    
   

Sample Volume (µl)

    
Automation

Automation Name

Setting

Value

Specification

     

Command line

bash -l -c ["]/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2:http} -u {username} -p {password} script:evaluateDynamicExpression -t true -h false -exp 'if (input.hasValue(::DNA Amount (ng)::)) { output.::Sample Volume (ul):: = float.parseFloat(step.::Desired DNA Amount (ng):: / input.::DNA Amount (ng)::)   ; output.::Nuclease-free water (ul):: = 30 - output.::Sample Volume (ul):: }' -log {compoundOutputFileLuid0}["]

Next Step = Set Next Step script to Advance

Trigger Location

Record Details

  
 

Trigger Style

Automatic upon exit

  
     

Command line

bash -l -c ["]/opt/gls/clarity/bin/java -jar /opt/gls/clarity/extensions/ngs-common/v5/EPP/ngs-extensions.jar -i {stepURI:v2:http} -u {username} -p {password} script:evaluateDynamicExpression -t false -h false -exp 'nextStep = ::ADVANCE::'  -log {compoundOutputFileLuid0}["]

Automatic Transition to Next Step