Note: This pipeline is currently being redeveloped to use Snakemake and Docker containers. ETA for this transition is Q4 2023.
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
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
MetaFunPrimer requires the following input files:
- Nucleotide and protein sequences of the genes of interest
- Metagenome files for your environment of interest
MetaFunPrimer is written and maintained by Paul Villanueva and Jia Liu.