Suppementary materials for our peer-reviewed scientific publications
hla-mapper
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hla-mapper was designed to minimize alignment errors on HLA genes typical of NGS analysis. Based on a database of known HLA sequences, each read pair is scored and assigned to the most likely locus. The final output is a BAM file with reads mapped to the human reference genome (hg38), enabling downstream analysis tailored to the user's needs. The resulting BAM file is far more reliable than those generated by using BWA, Bowtie2, or other mapping tools directly.
Download the source code and manual on GitHub
Download the hla-mapper database (hla-mapper 4).
Check the manuscript introducing this package.
Where it was first described: Hum Immunol. 2018 Sep;79(9):678-684.
kir-mapper
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kir-mapper is a toolkit for calling SNPs, alleles, and haplotypes for KIR genes from short-read second-generation sequencing (NGS) data. kir-mapper supports both single-end and paired-end Illumina sequencing data. It is compatible with Ion Torrent data uppon some adjustments.
Download the source code and manual on GitHub
Download the kir-mapper database
Check the manuscript introducing this package.
Where it was first described: HLA. 2025 Mar;105(3):e70092. doi: 10.1111/tan.70092.
VCFx
- VCFx comprises a set of tools for handling VCF (Variant Call Format) files, including converting phased VCF in complete fasta sequences. Download the source code and manual on GitHub