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SpecHLA reconstructs entire diploid sequences of HLA genes and infers LOH events. It supports HLA-A, -B, -C, -DPA1, -DPB1, -DQA1, -DQB1, and -DRB1 genes. Also, it supports both short- and long-read data.
This is a complete rewrite of a project originally written by Shane Killian & modified into PHP by Robert Webb & now I am converting it back to just use modern HTML5, CSS3 & JavaScript; cleaning it up and adding a few new bells and whistles.
Structural interpretation of Killer cell immunoglobulin-like Receptors (KIR) haplotypes from raw short or long read sequences. It predicts the presence/absence of 16 KIR genes and then uses that to predict pairs of structural (gene-content and order) haplotypes.
🌱🧬 Collection of scripts for the paper: "PAMP-triggered genetic reprogramming involves widespread alternative transcription initiation and an immediate transcription factor wave" (The Plant Cell 2022; PMID 35404429 🔗)