MHC Genotyper Illumina Short reads in select non-human primates.

Illumina Fastq file naming nomenclature

• MHC10001b_s80_L001_R1_001.fastq.gz
• MHC10001b_s80_L001_R2_001.fastq.gz
  • <Sample_ID>_s<SampleNumber>_L<LaneNumber>R<PairDirection><PoolNumber>.fastq.gz

Sample Sheet format:

Sample_ID,Sample_Name,Description,I7_Index_ID,index,Sample_Project,Species

Required and Pivot Table Columns:

• Sample_ID : (required string) Case-Sensitive. This is what illumina puts in the file name. And will be the "gs_id" in the pivot table
• Sample_Name : (required string) Case-Sensitive. This becomes the "Client_id" in the pivot table
• Species: (required string) Not case sensitive. The following are acceptable: Rhesus, Mamu, Pig-tailed, Mane, Cynomolgus, MCM.
• Comments: (optional, string) A comment that is added to the pivot table if it exists.
• Sample_Project: (require string) Case-Sensitive. Creates a separate pivotable for each Species/Sample_Project combination

Prerequisites:

Precompiled Pre Requisites:

• Debian, Ubuntu, or MacOSx required (not windows compatible)
  • Tested on MacOsx + Python 3.6.5 and Google Colab).
  • Python 3.7 and later (SHOULD) also work.
• download BBMAP_39.01.tar.gz and untar it (i.e. tar -xzvf BBMAP_39.01.tar.gz)
  • https://sourceforge.net/projects/bbmap/files/BBMap_39.01.tar.gz/download
• download vsearch with your appropriate OS, untar and create a symbolic link as needed
  • https://github.com/torognes/vsearch/releases
    • (i.e. tar -xzvf vsearch-2.21.1-macos-x86_64.tar.gz)

ln -s ~/vsearch-2.21.1-macos-x86_64/bin/vsearch /usr/local/bin/vsearch
ln -s ~/bbmap/bbduk.sh /usr/local/bin/bbduk.sh
ln -s ~/bbmap/bbmerge.sh /usr/local/bin/bbmerge.sh
ln -s ~/bbmap/bbmap.sh /usr/local/bin/bbmap.sh
ln -s ~/bbmap/stats.sh /usr/local/bin/stats.sh

Install more python libraries and apt-get prereqs.

pip install xlsxwriter
pip install pandas
pip install numpy
apt install -y pigz

Run The pipeline

python3 ~/github/mhc_genotyper/main.py \
--run_id 1234 \
--input_dir ~/BaseSpace/fastqReads \
--genotyper_root_dir ~/github/mhc_genotyper