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MetaFunPrimer

Note: This pipeline is currently being redeveloped to use Snakemake and Docker containers. ETA for this transition is Q4 2023.

Build Status

A pipeline to design high-throughput qPCR primers to target environmentally abundant genes. See the documentation for installation instructions and a demonstration of the pipeline.

Latest version: v0.90.4, 3/2/2020

Programs required

The versions listed after each program are those used in the testing of the pipeline.

  • CD-HIT (v4.6.8)
  • Diamond (v0.9.14)
  • Clustal Omega (v1.2.4)
  • BLAST (v2.7.1+)
  • EcoFunPrimer
  • Parallel

Instructions

MetaFunPrimer requires the following input files:

  • Nucleotide and protein sequences of the genes of interest
  • Metagenome files for your environment of interest

Authors

MetaFunPrimer is written and maintained by Paul Villanueva and Jia Liu.