Exome sequences are available from the sequence read archive (SRA) under BioProject PRJNA527214, and BioProject PRJNA529708.
Reference Sequences
The file IPD-Mamu-MHC-3Sept2018.gb.txt contains the Macaca mulatta (Mamu) sequences from the IPD database, downloaded on September 3, 2018. The Mamu entries were parsed using a simple python script
The file IPD_EXON2_9_3_2018.fasta contains sequences have been trimmed to the length of the MiSeq amplicons, and deduplicated. This IPD exon 2 reference file was used to compare genotyping results from the MiSeq and MES assays.
count_reads.py obtains number of reads extracted with our reference file
pivot_create.py creates a pivot table
sample_sheet_27.txt is a representative sample sheet of sequences to be analyzed.
make_genometyping_env.sh and and genometyping_file.sm creates a job submission, and a snakemake job
the text files beginning with 'HLA' were the parsed fasta files from HLA_e2_e4_reference_sequences.fasta for HLA class I and HLA class II, and the text file IPD_EXON2_9_3_2018.fasta contains the trimmed and deduplicated exon 2 sequences.
The Python Data Analysis Library Pandas was used for data analysis by all three methods that were discussed in the paper.
Supplementary Files
The file RheMac2.txt contains rheMac2 and HLA target coordinates that were used to prepare the combined minimal MHC and supplemental rhesus spike-in probe design.
The file Supplementary_Table_1_rev1.pdf contains the fraction of total exome sequence reads corresponding to MHC class I and class II genes after target capture with the VCRome2.1 probe design alone.
The file Supplemental_Figures_1_2.xlsx contains Supplementary Figures 1 & 2. Supplementary Figure 1 compares genotyping results from MiSeq PCR amplicon sequencing among all 27 animals with whole exome genotyping assays, using the DSR and SAVAGE strategies. Supplementary Figure 2 contains abbreviated Mamu-A, -B, and -DRB haplotype definitions for the animals that were evaluated in this study.
The Weatherall Report PDF describes regulations and guidelines outlined in the Animal Welfare Act, the Guide for the Care and Use of Laboratory Animals, and best ethical practices for scientific research involving animal subjects.