DRB3 and DRB5

[bsb2014]

Hi, can SpecHLA type DRB3 and DRB5 as kourami? Thanks

[wshuai294]

Hello, now SpecHLA does not support DRB3 and DRB5.

[bsb2014]

Do you have any plans to make SpecHLA support additional HLAs?

[bsb2014]

How does the SpecHLA phase the variants when only short reads are used? Thanks

[wshuai294]

Yes. Our group is developing another package to support additional HLA genes. I will let you know once it is finished.

[wshuai294]

If the short reads cannot afford enough phase information, SpecHLA will use HLA database, genotype frequency, and pedigree information to phase the variants.

[bsb2014]

It would be great if the next release could type HLA using diploid assembly. Thanks

[wshuai294]

Great suggestion. We do have some code to extract the sequence of HLA genes from the diploid assembly. I will update SpecHLA to support typing from diploid assembly as soon as possible.

[wshuai294]

Hello, Thanks for the valuable suggestion. As suggested, we added a module to support HLA typing from diploid assemblies (typing_from_assembly.py). Please see the changes in SpecHLA v1.0.3 or the latest commit.

[lidd77]

Yes. Our group is developing another package to support additional HLA genes. I will let you know once it is finished.

Hello, shuai, Are there any other tools can work for long read HLA typing ( nanopore sequencing) ? if we just add DRB3/4/5 imgt sequence into SpecHLA db , SpeckHLA can detect accurately DRB3/4/5 allele ?

Expecting your reply ! thanks .

[wshuai294]

Hello, Sorry for the delayed update. If you add DRB3/4/5 imgt sequence into SpecHLA db, it still needs some revisions in the scripts. I believe it will work well after some adjustments. I wonder do you have any benchmark data (with real data and ground truth)? With real benchmark data, we can add this function quickly.

Also, as I know HLA*LA also can work with nanopore sequencing data. But it might require too many computational resources. You can have a try on it.

Best, Shuai

[lidd77]

Hello, Sorry for the delayed update. If you add DRB3/4/5 imgt sequence into SpecHLA db, it still needs some revisions in the scripts. I believe it will work well after some adjustments. I wonder do you have any benchmark data (with real data and ground truth)? With real benchmark data, we can add this function quickly.

Also, as I know HLA*LA also can work with nanopore sequencing data. But it might require too many computational resources. You can have a try on it.

Best, Shuai

Yeah, I have got the benchmark data for A,B,C ,DRB1, DQA1,DQB1, DPA1, DPB1, DRB3/4/5 , that's why I hope you nice guy can support DRB3/4/5 as soon as possible .
could you update specHLA to support DRB3/4/5 this week ? Thank you very much !!!

[wshuai294]

So great! We will update it very soon. This week is a little challenging but I believe we can finish it next week. Could you please send us the benchmark data, so that we can start to adjust the parameters.

[lidd77]

So great! We will update it very soon. This week is a little challenging but I believe we can finish it next week. Could you please send us the benchmark data, so that we can start to adjust the parameters.

well, what is your email address ?

[wshuai294]

Thanks. My email is swang66-c@my.cityu.edu.hk

[lidd77]

Thanks. My email is swang66-c@my.cityu.edu.hk

have sent my email , please check that ,thanks

[alisamatisse]

Hello again @wshuai294 Shuai,

So is there an update to know if analyzed sequence contains DRB-3/4/5 and type it? :-)

Thanks!