###### tags: `Bioinformatics` # Consensus Prime ## Installation: 1. ```cd ~/Download``` 2. ```mkdir consensus_prime``` 3. execute ```wget https://github.com/mcollatz/ConsensusPrime/archive/refs/heads/main.zip``` in folder ```/Download/consensus_prime``` 4. execute ```unzip main.zip``` 5. copy all files to ```/usr/local/seqtools/consensus_prime/consensus_prime.py``` 6. set Path in ```/usr/local/seqtools/readme.sh``` > ```PATH=$PATH:/usr/local/seqtools/consensus_prime``` 7. conda env: ```conda create -n consensus_prime python=3.8``` 8. ```conda activate consensus_prime``` 9. ```conda install pandas``` Options if not installed on machine: ```sudo apt-get update -y``` ```sudo apt-get install -y mafft``` ```sudo apt-get install -y primer3``` ```sudo apt-get install -y clustalx``` For detailed informations and updates: https://github.com/mcollatz/ConsensusPrime ## Run: 1. ```conda activate consensus_prime``` 2. ```consensus_prime --help``` |command|what it does| |-|-| -i, --infile | Multi-Fasta file with gene sequences. [required] -x, --primer3 | Primer3 parameter file. [required] -o, --outdir | Specifies output directory. Default = . -t, --threads | Number of threads used by MAFFT. Default = -1 (all) -k, --keepduplicates | Keep duplicate sequences. Default = False -c, --consensusthreshold | Consensus threshold bitween 0 and 1 with 1 beeing a perfect consensus. Default = 0.95 -s, --consensussimilarity | Minimum similarity threshold for sequences in the input alignment when comparing each sequence to the consensus sequence. Default = 0.8 --primers | Known primers for visualisation in the final alignment in multifasta format. --negativesequences | File with sequences that get their consensus sequence added to the final alignment in multifasta format. -h, --help | show this message and exit 3. **execute following command:** ```consensus_prime.py --infile /path_to/your-data.fna --primer3 /path_to/primer3_parameters.txt``` ### Example for prime3 parameter-file: ``` SEQUENCE_ID= set by pipeline SEQUENCE_TEMPLATE= set by pipeline SEQUENCE_EXCLUDED_REGION= set by pipeline SEQUENCE_INTERNAL_EXCLUDED_REGION= set by pipeline PRIMER_TASK=generic PRIMER_PICK_LEFT_PRIMER=1 PRIMER_PICK_INTERNAL_OLIGO=1 PRIMER_PICK_RIGHT_PRIMER=1 PRIMER_OPT_SIZE=20 PRIMER_MIN_SIZE=15 PRIMER_MAX_SIZE=25 PRIMER_OPT_TM=52 PRIMER_MIN_TM=50 PRIMER_MAX_TM=54 PRIMER_INTERNAL_OPT_SIZE=30 PRIMER_INTERNAL_MIN_SIZE=25 PRIMER_INTERNAL_MAX_SIZE=35 PRIMER_INTERNAL_OPT_TM=64 PRIMER_INTERNAL_MIN_TM=60 PRIMER_INTERNAL_MAX_TM=68 PRIMER_PRODUCT_SIZE_RANGE=50-1000 PRIMER_TM_FORMULA=1 PRIMER_EXPLAIN_FLAG=1 PRIMER_SECONDARY_STRUCTURE_ALIGNMENT=1 PRIMER_THERMODYNAMIC_OLIGO_ALIGNMENT=1 PRIMER_THERMODYNAMIC_TEMPLATE_ALIGNMENT=1 PRIMER_NUM_RETURN=10 PRIMER_MAX_HAIRPIN_TH=47.0 PRIMER_INTERNAL_MAX_HAIRPIN_TH=47.0 PRIMER_MAX_END_STABILITA=100.0 = ``` For detailed informations and updates: https://primer3.org/manual.html