which is the best software for Sequence based typing(SBT) HLA typing?

Question

[Shashi Kanth]

Among Connexio Assign SBT, Utype and GenDx SBT which is the best software for HLA typing

Best answers are entertained.

Thank you

[mikhail.shugay]

Check out this post: Software For Hla Typing Using Ngs?

Answer 1

[GouthamAtla]

It depends on the type of data.

If you are using illumina which would cover all the exons of MHC-I and MHC-II, there are many opensource software which gives 8 digit accuracy. E.g ATHLATES, SOAP-HLA,.

If you have Roche amplicon sequence data, which covers only exon2,3(MHC-I) and exon 1(MHC-II), there are no open source softwares available which could give 8-digit accuracy.

All the platforms have their own recommendations for HLA-typing commercial software. Roche and illumina recommends connexio, pacbio recommends ISO-SEQ.

PS: We had roche data for pilot studies (around 100 known samples) and used Connexio which gave us almost accurate results. I also used HLACaller for the same data and got similar results. but only 4 digit accuracy.

[gskbioinfo143]

Hi sir

at current scenario among Omixon, NGSengine, NxType which one is best for NGS HLA Typing using Ion Torrent Platforms

Thanks