Figure 1 | Scientific Reports

Figure 1

From: Targeted analysis of polymorphic loci from low-coverage shotgun sequence data allows accurate genotyping of HLA genes in historical human populations

Figure 1

Different steps performed by the TARGT pipeline for HLA genotyping of ancient and modern samples. Preprocessing (optional): after quality control, genomic sequences are pre-processed (adapter clipping, merging and trimming) using ClipAndMerge (version 1.7.3) from the EAGER pipeline55. Mapping: performed using Bowtie249 against a comprehensive reference file, containing known 3rd field HLA alleles (following G-group nomenclature). Sorting: mapped reads are grouped by gene specificity and saved into gene-specific FASTA files. HLA genotyping: Sample-specific FASTA files are manually analyzed using BioEdit50 to genotype HLA genes in ancient and modern samples.

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