In our lab we're studying T-cell receptor repertoires and now are planning to complement this data with HLA-typing for huge cohorts of patients. I was wondering if there are people around here who do HLA typing using NGS can answer several questions.
- Is there any reliable non-commercial and open software to determine HLA alleles from NGS data from Illumina platform?
- Do you use commercial solutions, such as Omixon HLA typing?
- What is your experience with commercial software that claims accurate processing of data from multiple platforms (Illumina, 454, IonTorrent, PacBio) like 157-P:NGSEngine. Is it really possible to correctly determine alleles with Illumina HiSeq reads?
Thanks in advance,