Optitype hla分型结果

Author: mxpr

August undefined, 2024

Web最近又被抓去做HLA分型，由于各种原因之前通过singularity安装在超算上的optitype用不了了，只好用conda安装optitype再解决之前说的conda安装后的报错问题了。我首先是在超算上进行了optitype的conda安装，装好之… WebAug 20, 2014 · Result: We present OptiType, a novel HLA genotyping algorithm based on integer linear programming, capable of producing accurate predictions from NGS data not …

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WebApr 14, 2024 · Optitype的一个问题是只能进行HLA-A、HLA-B、HLA-C等三个class I基因。不过在一些文章中，Optitype的表现要比seq2HLA好。 Optitype的运行需要python2（我实 … WebOct 11, 2024 · OptiTypePipeline.py -i read_1.fq read_2.fq --dna -v -o optutype. 1. AMD YES的r7-4700u加持下，在近乎突破硬件极限的情况下完成了分型。. 结果首先是个pdf文件，是 … floral installation artists

HLA分型软件Optitype - 生物信息文件夹 - GitHub Pages

WebDec 1, 2014 · To summarize, OptiType is a fast and accurate HLA typing method based on NGS data, which provides an alternative approach to common HLA genotyping methods. … WebJun 14, 2024 · HLA(human leukocyte antigen ，人类白细胞抗原)是人类的主要组织相容性复合体（MHC）的表达产物，该系统是所知人体最复杂的多态系统。 HLA-I类分子：内源性 … WebMar 7, 2024 · OptiType(2014年) —— 基于整数线性规划的HLA基因分型算法 [PMID: 25143287] xHLA (2024年) [PMID：28674023] （听说对硬件要求较高; HLA-HD (2024年) … floral installations phoenix paper flowers

(PDF) A New Human Leukocyte Antigen Typing Algorithm

WebJun 10, 2024 · OptiType is a novel HLA genotyping algorithm based on integer linear programming, capable of producing accurate 4-digit HLA genotyping predictions from NGS data by simultaneously selecting all major and minor HLA Class I alleles. Environment Modules. Run module spider optitype to find out what environment modules are available … WebJul 19, 2024 · HLAminer软件可以同时对HlA I型基因和II 型基因进行分型，但是分型结果中不可避免的会存在假阳性的结果。. 为了提高分型结果的准确性，不同的研究团队都在开发 … floral instant downloadWebMay 31, 2024 · Precision HLA typing from next-generation sequencing data - Issues · FRED-2/OptiType. Precision HLA typing from next-generation sequencing data - Issues · FRED-2/OptiType. Skip to content Toggle navigation. Sign up Product Actions. Automate any workflow Packages. Host and manage packages Security. Find and fix vulnerabilities ... greatsealcoating.com

"Web2.optitype输入文件【存储空间占用低】：可以先在超算上对WES/RNA-Seq测序数据进行razers3比对提取和samtools格式转换(详见之前的文章生科院的老张：服务器singularity … " - Optitype hla分型结果

Optitype hla分型结果

GitHub - FRED-2/OptiType: Precision HLA typing from next …

Web我们首先使用 HLA-HD、Athlates 和 OptiType 对 HLA 的 I 型和 II 型共计 12 个标准品分析，具体结果见表 3。 HLA-HD 和 Athlates 比 OptiType 的 HLA I 型分型更加准确，两者仅 …

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WebNov 12, 2024 · HLA typing benchmarking using data from the 1000 Genomes Project confirmed the high performance of OptiType and HLA-HD, especially on RNA-seq data (Supplementary Figs S2–S4). DNA-seq calls showed a lower accuracy, a systematic underestimation of zygosity and a higher number of missing calls likely due to the low … WebNov 29, 2024 · Hi, Why I don't get HLA typing of all the genes (A, B and C) in a single run? Rather, I have to run multiple times to get that (as shown below). I wonder if its bug. And, do you think removing duplicate reads from input files (.bam) is w...

WebMay 20, 2024 · The accuracy of HLA-Ia typing by OptiType can reach 100% with the average depth of HLA gene regions >20x. Besides, the accuracy of 2-digit and 4-digit HLA-Ia typing based on control samples was higher than tumor tissues. In conclusion, OptiType by using WES data from control samples with the high average depth (>20x) of HLA gene regions … WebJan 8, 2015 · HLA-I类基因分型软件-Optitype介绍. HLA（human leukocyte antigen ，人类白细胞抗原）是人类的主要组织相容性复合体（MHC）的表达产物。. 通常也称为人类主要组织相容性复合物 (MHC)，在染色体 6p21.3 上包含一个 4 Mb 的区域，其中包含 200 多个基因。. HLA根据不同的基因位 ...

Web1991年第11届国际hla专题讨论上提出了hla的dna分型方法，这类方法近年来在研究和应用方面发展非常快，有取代其他方法的趋势。dna分型方法主要分为两种：基于核酸序列识别 … WebJun 25, 2024 · Results: We tested two widespread HLA typing methods using high quality full genome sequencing data from 150 individuals in 50 family trios from the Genome Denmark project. First, we computed descendant accuracies assessing the agreement in the inheritance of alleles from parents to offspring. Second, we compared the locus-specific …

WebMay 20, 2024 · For both WES data and RNA-seq data, OptiType showed the highest accuracy for HLA-Ia typing than the other 3 programs at 2-digit and 4-digit resolution. Additionally, …

WebJan 8, 2015 · NGS-based HLA typing algorithm. Image. Pulls 10K+ Overview Tags. OptiType. Precision HLA typing from next-generation sequencing data. Authors: András Szolek, Benjamin Schubert, C great seal certificationWebNational Center for Biotechnology Information great seal coatingOptiType uses the following software and libraries: 1. Python 2.7 2. RazerS 3.4 3. SAMtools 1.2 4. HDF5 1.8.15 5. CPLEX 12.5or other Pyomo … See more Optional step zero: you might want to filter your sequencing data forHLA reads. Should you have to re-run OptiType multiple times on the same sample(different … See more OptiType is a novel HLA genotyping algorithm based on integer linearprogramming, capable of producing accurate 4-digit HLA genotyping predictionsfrom NGS data by simultaneously … See more floral institute shoppingWeblinux-64 v1.3.2; noarch v1.3.5; conda install To install this package run one of the following: conda install -c bioconda optitype conda install -c "bioconda/label/cf202401" optitype floral installation weddingWebDec 17, 2024 · 상기 방법은: 피검체 유래의 생물학적 시료로부터 획득된 DNA 또는 RNA에 대한 염기 서열 분석을 수행한 결과를 획득하는 단계, 및 OptiType, HLA-HD, PHLAT, HLAscan, 및 HLA*LA 중 3개 이상의 툴(tool)들을 사용하여, 상기 염기 서열 분석의 결과로부터 HLA 타입을 결정하는 ... great seal bugWebJul 14, 2024 · OptiType, Phlat and Polysolver were used to execute HLA typing from WES data, while OptiType, Phlat and seq2hla were utilized for RNA-seq data. As shown in … floral institute seattleWebOct 1, 2024 · The availability of HLA genotyping was the highest in the OptiType tool for all HLA-A, C, and B types, and the values were 99.1% for HLA-A, 99.4% for HLA-B, and 100% for HLA-C. In HLA-A and HLA-C, Kourami showed the lowest availability, and the values were 72.6% and 72.5% in each. great seal campground