Usage from command line

IMPI is also available as command line tool. Please download the IMPI Command Line Tool in the Download section.

The command line usage of IMPI allows for pre-processing (prep) and allele frequency calculation (proc). Please be sure to define paths to NGmerge, Bowtie2, the Bowtie2 library and clinical relevant mutations (optional) in the settings file!

Pre-processing

python IMPI_cmd.py prep -i PATH_TO_FILE.fastq [-i2 PATH_TO_FILE_R2.fastq] -ref REFERENCE_SEQUENCE -p1 PRIMER1 -p2 PRIMER2 -r READ_LENGTH -s START_POSITION

Parameters

-i input file

-i2 second input file (if paired-end files)

-ref reference sequence (raw sequence or FASTA file)

-p1 forward primer

-p2 reverse primer

-r exact read length

-s start position in reference sequence

-NGm NGmerge: min/max overlap (in case of paired-end reads) (default: 10)

-NGp NGmerge: allowed missmatch rate (in case of paired-end reads) (default: 0.1)

-o output filename (default: current datetime and current directory)

Allele frequency calculation

python IMPI_cmd.py proc [OPTIONS] PATH_TO_FOLDER

Parameters

-q min quality (default: 33)

-u min UMI quality (default: 33)

-c min clustersize (default: 1)

-co min cut-off (default: manual)

-cov min cut-off value (default: 0.5)

-n max N (default: 3)

-r min reference sequence identity (default: 0.90)

-m max mismatches (default: 3)

-i max insertions (default: 1)

-d max deletions (default: 1)

-o omit from UMI (default: 0)

-e/--export definition of PWMs to export to csv files: [u, c1, c2] (u…unclustered, c1…clustered1, c2…clustered2) (default: [u, c1, c2])

-mut export clinical relevant mutation PWM (default False)