Script to design outward specific primers at the end of the contig sequences.

Under development

　 　

Requirements

You must have the following installed on your system to use use this cript:

• linux os
• python3(>3.6)
• primer3 (https://github.com/primer3-org/primer3)
• primer3 masker (https://github.com/bioinfo-ut/primer3_masker)
• bbmap (https://github.com/BioInfoTools/BBMap)
• genometester4 (https://github.com/bioinfo-ut/GenomeTester4)
• spades (https://github.com/ablab/spades)
• biopython (https://github.com/biopython/biopython)
  optional

Without installing assemblyP (recommnended)

mamba create -n assemblyP -y python=3
conda activate assemblyP
mamba install -c bioconda primer3==2.5.0 bbmap genometester4 spades==3.15 -y
pip install biopython
git clone [email protected]:kazumaxneo/assemblyP.git
  
#Then, run assemblyP.py
python assemblyP/assemblyP.py -f paired_1.fq.gz -r paired_2.fq.gz

Install dependency and assemblyP script (developing)

#Setup virtual enviroment using conda or mamba
#If you already have Anaconda or Minicona enviroment, you can install mamba with conda.   
conda install -c conda-forge mamba -y

#Then, create virtual enviroment
mamba create -n assemblyP -y python=3.9
  
#Activate enviroment
conda activate assemblyP
  
#Install dependancy
mamba install -c bioconda primer3==2.5.0 bbmap genometester4 spades==3.15 -y
    
#Clone repository and install assemblyP package
git clone https://github.com/kazumaxneo/assemblyP.git && cd assemblyP/
pip install .

help

$ assemblyP -h

usage: python part1-change.py -f paired_1.fq.gz -r paired_2.fq.gz  
Script to design outward specific primers at the end of the contig sequences (v0.1)  

optional arguments:  
  -h, --help          show this help message and exit  
  -c <contigs.fasta>  contig fasta file  
  -f <forward reads>  paired read 1  
  -r <reverse reads>  paired read 2  
  -o PATH             output directory name  
  -k 16               K-mer size for rpeat masking.  
  -g PATH             spades contig name  
  -l PATH             glistmaker output file  
  -m PATH             repeat masked file  
  -n PATH             border sequences    

test run

cd test_data/
#perform de novo aassembly and make primers
assemblyP -f paired_1.fq.gz -r paired_2.fq.gz

#make primers using preassembled sequences
assemblyP -f paired_1.fq.gz -r paired_2.fq.gz -c ontigs.fasta

Docker

Under development

　 　

Licence

GPL v3.