Analyse mutations

This pipeline has been set up in order to compute the mutations and their frequencies caused by CRISPR from a collection of different sample of maize protoplast. This pipeline is in python and can be used with python 3.0

Program version

This pipeline use different other tools, here is the version of the different software used.

• PEAR : version 0.9.10
• FastQC : version 0.11.7
• Fastq-mcf : version 1.04.676
• Needle (EMBOSS) : version 6.6.0.0

Argument of the pipeline

This pipeline take some arguments as entry some are needed and other are optional.

• -h or --help : show help message and exit
• -f or --forward (required): forward file of the reads for the assembly
• -r or --reverse (required): reverse file of the reads for the assembly
• -a or --adapters (required): fasta sequence of the adapters
• -t or --target (required): fasta sequence of the target sequence for the alignment
• -p or --primer (required): fasta sequence of the primer (as to be the same number of file as the sequence target)
• -pam (required): position of the first base of the pam sequence (used to know the crispr range)
• -o or --directory (optional): path to the output results (default : /output_program/)
• -cutoff (optional)(0-1): cutoff for the frequency logo (default : 0.0001)
• -score (optional)(0-350): minimal alignment score required for the analyse (default : 200), can't be superior to 350
• -d or --direction (required) (sens,antisens,forward,reverse): direction of the pam sequence (as to be the same number of file as the number of pam position)

Code line

./Projet_CRISPR_MAIS/analyse_mutations.py -f NP06_S6_R1_001.fastq -r NP06_S6_R2_001.fastq -t NP06_ZmKAK1_KAK1_233_L1750.fasta -a data/adaptors.fa -p primers_NP06.txt -pam 93 -d sens