Optitype使用

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August undefined, 2024

WebJul 19, 2024 · opitype利用HLA I型基因exon2到exon3的DNA序列构建了一个参考数据库，如果reads能够比对到这个参考数据库，认为这些reads来自与HLA基因。. 用法如下. docker … WebSep 10, 2024 · Optitype :只对ABC进行分型，据报道准确率较高，开发团队贴心地提供了在线版本。使用效果是对ABC的分型结果不错，目标区域测序数据分析耗时在1小时左右。幸亏有在线版，自行编译安装，bioconda安装和docker都会报错。 ...

Investigations of sequencing data and sample type on HLA class …

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 … WebOct 11, 2024 · Optitype软件安装最开始尝试使用docker，无奈悲剧的失败，发现bioconda有这个软件的，于是上conda，感觉比docker更方便呢。还有一个好处是，win10家庭版不 … canadian art preservation foundation

Issues · FRED-2/OptiType · GitHub

WebNGS-based HLA typing algorithm. Container. Pulls 10K+ Overview Tags. Dockerfile ################################################################# # Dockerfile ... 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 WebJun 7, 2024 · For example, OptiType drops alleles that are not present in HLA databases, and HLAProfiler only selects the top n pairs by proportion of explained reads. Taking inspiration from HISAT-genotype, arcasHLA uses allele transcript quantification combined with culling of low-support alleles to narrow down the pool of possible alleles, thereby ... canadian art contests 2018

Optitype使用

Evvail HLA-I类基因分型软件-Optitype介绍 Omics - Hunter

WebJul 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 Figure 1, the accuracy of OptiType, Polysolver and Phlat for 4-digit HLA typing of WES data was 99.11%, 95.83% and 93.75%, respectively. Accuracy of OptiType, Phlat and seq2hla from … WebSep 10, 2024 · Optitype :只对ABC进行分型，据报道准确率较高，开发团队贴心地提供了在线版本。使用效果是对ABC的分型结果不错，目标区域测序数据分析耗时在1小时左右。幸 …

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WebApr 14, 2024 · Optitype的运行需要python2（我实测使用python3也能成功运行），RazerS，samtools，HDF5，CPLEX（由于CPLEX是个商用软件，建议使用GPLK代 … WebDec 1, 2014 · We present OptiType, a novel HLA genotyping algorithm based on integer linear programming, capable of producing accurate predictions from NGS data not …

WebMay 10, 2024 · opitype的使用分成以下两步： 1. 采用 razers3 比对参考序列数据库. razers是一款比对工具，可以从原始的测序数据中筛选出属于HLA基因的reads。opitype利用HLA I … WebUsage. To see the list of available tools, simply enter arcasHLA.To view the required and optional arguments for any of the tools enter arcasHLA [command] -h.. extract: Extracts reads mapped to chromosome 6 and any HLA decoys or chromosome 6 alternates.; genotype: Genotypes HLA alleles from extracted reads (no partial alleles).; partial: …

WebJan 8, 2015 · 目前有两种方式来安装 Optitype ： 1、基于docker. 如果有docker，那就比较简单了，直接：docker pull fred2/optitype. 然后执行：docker run -v … WebAug 20, 2014 · OptiType is applicable to NGS data of different sources and outperforms previously published in silico HLA typing approaches on both two- and four-digit resolution. The latter is especially important in clinical applications like individualized vaccine design, prevention of graft-versus-host disease and treatment of autoimmune diseases. ...

Web我们也做了一些原创性工作，在测试时发现OptiType有时会运行错误，便开发了一个补丁来解决这个问题，让OptiType能够稳定运行得到分型结果。另外，我们还基于打分策略开发了一个工具，整合肿瘤和对照样本的多个分型工具的分型结果，让分型准确性达到99.9% ...

WebNov 29, 2024 · OptiType result output · Issue #85 · FRED-2/OptiType · GitHub. FRED-2 / OptiType Public. Notifications. Fork 69. Star 150. Issues 41. Pull requests 3. Actions. Projects. fisher et al 2009WebDec 16, 2024 · conda install optitype 或者 docker pull fred2/optitype. 在使用OptiType进行HLA分析之前，建议先过滤出待分析序列中的HLA序列，这将能节省程序的运行时间，官方推荐使用RazerS3来进行比对，不过该软件会将序列读入到内存中，所以需要机器内存比较大。 fisher estates ingleside ilWeb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 … canadian artist debra bernierWebJun 14, 2024 · optitype需要先利用razers3先过滤一下reads，把和HLA相关的序列提出来，然后在运行optitype进行分型，从而加快分析速度。第一步，Razers3 1 fisher et control valvesWebInteractive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs. Allocate an interactive session and run the program. Sample session (user input in bold ): [user@biowulf]$ sinteractive --cpus-per-task 4 --gres lscratch:10 salloc.exe: Pending job allocation 46116226 salloc.exe: job 46116226 queued and ... canadian artistic food expoWebMay 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, HLA typing accuracy from WES data was higher than from RNA-seq data (99.11% for WES data versus 96.42% for RNA-seq data). The accuracy of HLA-Ia typing by OptiType can … fisher et al. 2020Weblinux-64v1.3.2. noarchv1.3.5. conda install. To install this package run one of the following:conda install -c bioconda optitype. conda install -c "bioconda/label/cf202401" … canadian artist ted harrison