This repository contains all code to reproduce the analysis in the article "Development and evaluation of a rapid and cost-efficient NGS-based MHC class I genotyping method for macaques by using a prevalent short-read sequencer".
- blastn
- cutadapt
https://cutadapt.readthedocs.io/en/stable/ - python (version >= 3.7)
- perl 5
(1) Please copy MHC_genotyping or MHC_denovo(for novel allele detection) directory to your computer.
(2) Please copy fastq file to MHC_genotyping directory.
(3) Please move MHC_genotyping or MHC_denovo directory and run .sh file like below.
$ sh pipeline/MHC_pipeline_v5.sh
$ sh pipeline/MHC_pipeline_denovo_v3.sh (for novel allele detection)
(4) Please enter information following the instructions on the screen.
enter Fastqfile: Please enter Fastq file name.
enter Mamu or Mafa: Please enter species Mamu (Rhesus Macaque) or Mafa (Cynomolgus Macaque).
enter runid (any characters): Please enter any characters.
enter barcodeid (any characters): Please enter any characters, with a barcode ID number recommended for Ion sequencer.
enter samplename (any characters): Please enter any characters.
(5) result file name is "(samplename entered from terminal)_result.txt"