cliu32/athlates

ATHLATES

Abstract: ATHLATES (accurate typing of human leukocyte antigen through exome sequencing) was originally developed to analyze whole-exome sequencing (exome-seq) data from the Illumina platform and to predict the HLA genotype at 2-field or higher resolution. HLA locus-specific reads are first collected by stringent read mapping to the IMGT/HLA database. ATHLATES then performs read assembly, candidate allele identification, and genotype inference. Here we describe the protocol of using ATHLATES for the above purpose and expand the application to analyze targeted sequencing data using amplicons of full HLA genes.

This repository supplies scripts for running ATHLATES. A sample dataset generated by amplicon shotgun sequencing on the Illumina platform is also provided. Reference protocol: submitted and under review (10/2/2017).

athlates's Issues

Where to download Athlates?

Hi Liu,
Your Athlates is very useful to predict the HLA type. But unfortunately, I don't find where to download it.
Can you provide the link of Athlates when you have free time?
Thank you very much!

Best,
Xiongbin

can discover new allele

Hi, cliu32
so sorry to boring you again.
Can athlates find new hla allele ? And wether there is a new version of athlates ?

hla database updata

Hi,cliu32
After i updata hla database to 3.46, I met an error "err: process_block: block size != refs size" when i use athlates typing function. I try some times and still get this error.
could you give me some advices ?

Athlates download

Hi,
I submitted my information in the download page: https://www.broadinstitute.org/viral-genomics/viral-genomics-analysis-software-registration
but I got an error massges:
"An illegal choice has been deteced. Please contact the site administrator."