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HLA alignment, approximation and frequencies

Hello, I have tried aligning this fastq file (long reads from ONT sequencing) with minimap2. I came up with a sam file, converted to bam file, sorted and indexed it. I want to come up with HLA types and frequencies, but stuck here.... It seems some key steps enter code here

$ minimap2 -ax map-ont A_gen.fasta HLAs.fastq > HLA.sam
$ samtools view -Sb -o HLA.bam HLA.sam
$ ls
$ samtools sort -o HLA-sorted.bam HLA.bam
$ samtools index HLA-sorted.bam
fastq
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updated by Kevin Blighe Kevin Blighe • written by oumo • oumo

Hi, to proceed with HLA typing and determining frequencies, you can use specialized tools designed for this purpose. Here are a few options: 1) OptiType ; 2) SpecHLA.

They works with both short and long reads and allow you to extract HLA-specific reads and then obtain typing. I'm not an expert in downstream analysis of this type but just do a search and you'll find something about it. I hope I have been of help to you.

Regards,

Marco

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written by marco.barr • marco.barr

Thank you Let me check out these specialized tools

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written by oumo • oumo

1 answer

Hi oumo,

Your alignment pipeline looks solid for mapping ONT reads to the HLA-A reference, but to extract specific allele types and their frequencies, you'll need a dedicated HLA typing tool that handles long reads. I recommend SpecHLA, which processes your sorted BAM directly and outputs diploid genotypes along with read support counts for frequency estimation—run it via their long-read mode script on the BAM and a full IMGT HLA reference. This should resolve your bottleneck without much extra setup.

Kevin

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written by Kevin Blighe Kevin Blighe

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