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

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

Best answers are entertained.

Thank you

sbt

1 answer

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.

Hi sir

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

Thanks

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