MetaFunPrimer: qPCR primer design pipeline to target function

MetaFunPrimer is a primer design pipeline designed to target genes and functions within an environment.

1. mfpcluster: The input genes are clustered using CD-Hit. A similarity level is recommended.
2. mfpsearch: Searches for the input genes against reference files.
3. mfpcount: Summarizes the results of mfpsearch by counting the presence and abundance of the input genes in the reference files. mfpcount will also recommend which clusters to include in the final primer design process.
4. mfpprepare: Formats and prepares a fasta file for input into the next step.
5. mfpdesign: Primers are designed using EcoFunPrimer.
6. mfpqpcr: Performs in silico qPCR to determine primer effectiveness and specificity.

Contents:

• Installation
  • Requirements
• Tutorial
  • Determining optimal clustering threshold: mfpcluster
  • Counting presence and abundance: mfpsearch
  • Determining environmentally representative genes: mfpcount
  • Preparing fasta files for primer design: mfpprepare
  • Designing primers: mfpdesign
• Documentation
  • mfpcluster
• Troubleshooting and Support
  • Frequently Asked Questions
  • Contact
• License

Indices and tables

• Index
• Module Index
• Search Page