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What's the use of HLAreporter software?

2025-01-18 Update From: SLTechnology News&Howtos shulou NAV: SLTechnology News&Howtos > Internet Technology >

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This article mainly shows you "what is the use of HLAreporter software", the content is easy to understand, clear, hope to help you solve your doubts, the following let the editor lead you to study and learn "what is the use of HLAreporter software" this article.

In the previous article, we introduced the naming format of HLA Allel in detail, as shown in the following diagram

As can be seen from the schematic diagram, a HLA Allel can be divided into four fields, with the final modified suffix, a total of five fields; when defining the resolution of the HLA typing result, it will be judged according to the maximum number of digits of the typing result. If only field 1, that is, the information of serological classification, is given, it represents the typing result of 2 digits; if field 2, that is, the corresponding protein information, is given at most, it represents the typing result of 4 digits. If field 3, that is, CDS area information, is given at most, it represents an 8-bit typing result; if the typing result gives a final suffix, it represents a 9-bit typing result.

There are many technical methods for HLA typing, such as chip, high-throughput sequencing, etc.; the HLA Allel resolution identified by different means is different, if only 2-bit typing result is given, it belongs to low resolution; if 4-bit typing result is given, it belongs to medium resolution; 8-bit or more typing result can be given, which belongs to high resolution.

This paper mainly introduces the HLA reporter software, which can use the results of high-throughput sequencing for HLA typing. The result of typing has a high resolution, up to 9 digits at most. The following figure shows the result of comparison between this software and other similar software.

It can be seen that in the test sample, the HLAreporter software typing result is due to the result of HLAminer. The screenshot is from the official literature and the link is as follows

Https://genomemedicine.biomedcentral.com/articles/10.1186/s13073-015-0145-3

The official website of the software is as follows

Http://paed.hku.hk/genome/software.html

The installation process is as follows

Wget http://paed.hku.hk/genome/software/HLAreporter.zipunzip HLAreporter.zipcd HLAreporter.v103

HLAreporter.sh is the running script of the software. The principle is as follows

Because of the polymorphism of HLA, it is not possible to directly compare the reads to the reference genome. HLAreporter designed a CRP (comprehensive reference panel) reference genome, and the CRP was constructed with reference to the known HLA Allel information in the IMGT/HLA database. The reads was compared with the CRP through bwa to extract the reads of a HLA gene, and then assembled, the assembled contig was compared with the database to determine the final Allel.

The usage of the software is as follows

Bash HLAreporter.sh test HLA_B test.R1.fq test.R2.fq

The first parameter test represents the sample name; the second parameter represents the detected HLA gene, and the third and fourth parameters represent the fastq sequence that is sequenced at both ends.

The whole pipeline is divided into three parts

1. Bwa compares CRP database

When you provide the original fastq data, the 4digit_map_HLA.sh script is automatically called for comparison.

The core content of the script is as follows

Bwa aln exon23_high_resolution_multi_ref.fa $1 > $3_1_exon23_high_resolution_multi_ref.saibwa aln exon23_high_resolution_multi_ref.fa $2 > $3_2_exon23_high_resolution_multi_ref.saibwa sampe exon23_high_resolution_multi_ref.fa $3_1_exon23_high_resolution_multi_ref.sai $3_2_exon23_high_resolution_multi_ref.sai $1 $2 > $3_exon23_high_resolution_multi_ref.samsamtools view-bS $3_exon23_high_resolution_multi_ref.sam > $3_exon23_high_resolution_multi_ref.bamsamtools view-b-F 4 $3_exon23_high_resolution_multi_ref.bam > $3_exon23_high_resolution_multi_ref_mappedreads.bamsamtools sort $3_exon23_high_resolution_multi_ref_mappedreads.bam $3_exon23_high_resolution_multi_ref_mappedreads_sortedsamtools index $3_exon23_high_resolution_multi_ref_mappedreads_sorted.bam

$1 and $2 correspond to the R1 and R2 reads of double-terminal sequencing, respectively. $3 represents the sample name. By calling bwa sampe, the original double-terminal reads is compared with exon23_high_resolution_multi_ref.fa to generate an exon23_high_resolution_multi_ref_mappedreads_sorted.bam file.

two。 Identify HLA Allel

For the three type I genes HLA-A, HLA-B and HLA-C, the 4digit_predict_classI_ssake.sh script is called; for the HLA II type gene, the 4digit_predict_classII_main.sh script is called.

3. Give the frequency of Allel in different populations.

Using the information in ANFD database, the frequency of each Allel in different groups is given, which is realized by script HLAfreq.sh.

The final output is saved in the results directory, as shown below

-HLAreporter version 1.03Report createdFri Apr 17 11:24:24 HKT 2015 Murray- -- Allele DRB1*01:01:01GAllele DRB1*04:07:01GPhase DRB1*04:08:01Alleles detectedDRB1*01:01:01GDRB1*01:17DRB1*04:08:01DRB1*04:07:01GGap location:97 208Non-polymorphic gap:111 bpHLA data quality profile:10xcov% 100 20xcov% 100 30xcov% 97 50xcov% 89- -HLA allele frequencyFour populations in Europe China Japan Africa are shownBy allele frequency net database (www.allelefrequencies.net)- [Allele] [EUR] [CHN] [JPN] [AFR] DRB1*01:01 0.0860 0.0230 0.0582 0.0130DRB1*04:07 0.0112 0.0030 0.0057 0.0030DRB1*04:08 0.0039 0.0020 0.0000 0.0000DRB1*01:17 0.0000 0.0000 0.0000

HLAreporter currently supports only the typing of the following 11 genes

HLA_A

HLA_B

HLA_C

HLA_DRB1

HLA_DRB2

HLA_DRB3

HLA_DRB4

HLA_DRB5

HLA_DQB1

HLA_DPB1

HLA_DQA1

The above is all the contents of the article "what is the use of HLAreporter Software?" Thank you for reading! I believe we all have a certain understanding, hope to share the content to help you, if you want to learn more knowledge, welcome to follow the industry information channel!

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