Optitype使用

WebMay 31, 2024 · Precision HLA typing from next-generation sequencing data - Issues · FRED-2/OptiType Web关于 GitLab GitLab：DevOps 平台 浏览 GitLab 安装 GitLab 定价 与专家交谈 /

OptiType/README.md at master · FRED-2/OptiType · GitHub

Web与使用单个read相比，使用组装的contig可以大大减少给定序列信息的等位基因预测的模糊性。 HLA类型推断过程通常是通过各种计算方法来解决优化问题，例如贪婪算法（例如seq2HLA）、整数线性规划（例如 Optitype） … WebJan 8, 2015 · Furthermore, depending on your settings in config.ini you can choose to keep the bam files OptiType produces when all-mapping reads against the reference: these will be stored in the output directory of your current run.. Then, if you want to re-run OptiType on the same sample, you can give it those intermediate .bam files as input instead of .fastq files, … dachshund pups for sale online https://quingmail.com

丁伟/OptiType - Gitee

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: … Weblinux-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" … WebJan 8, 2015 · OptiType is a novel HLA genotyping algorithm based on integer linear programming, capable of producing accurate 4-digit HLA genotyping predictions from … dachshund purses sale womens

HLA--polysolver - 简书

Category:28个样本，4种不同分析方法的比较发了9分？ - 腾讯云

Tags:Optitype使用

Optitype使用

文章发表 肿瘤患者HLA分型，“裕”加精准！-裕策生物

WebApr 25, 2024 · 其中HLA分型可使用Optitype、Polysolver、HLA-HD、HLAscan、seq2HLA等获得。从我目前的使用感受来说，数据量比较小的时候用Optitype，数据量大的时候 … WebJun 25, 2024 · 使用全外显子组测序（wes）检测hla基因中的体细胞突变受到hla基因座的高度多态性的阻碍。 描述一种计算管道，其能够准确推断I类HLA-A，-B和-C基因的种系等位 …

Optitype使用

Did you know?

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。 ... 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 …

WebDec 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。 WebNov 12, 2024 · nextNEOpi infers class-I and -II HLA types from WES/WGS (DNA-seq) and RNA-seq data using OptiType (Szolek et al., 2014) and HLA-HD (Kawaguchi et al., 2024), respectively, and can employ an RNA-seq-informed strategy to correct DNA-seq calls for missing HLA genes or alleles (Supplementary Methods).HLA typing benchmarking using …

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 … 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 …

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 binks a dim-witted character from star warsWeboptitype¶ Precision 4-digit HLA-I-typing from NGS data based on integer linear programming. Use razers3 beforehand to generate input fastq files only mapping to HLA-regions. dachshund puzzle toysWebJun 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 … dachshund pyjamas for dogsWebNov 22, 2024 · 使用Fastp对原始测序数据进行质量控制后，用OptiType、Phlat、Polysolver对WES数据执行HLA分型，用OptiType、Phlat和seq2hla对RNA-seq数据执行HLA分型，分别与基于SMRT技术的PCR-SBT方法获得HLA基因分型数据进行比较和准确性评估，从而对分型工具进行了性能评价，最终确定了 ... binks air compressor filterWeb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% ... dachshund purses leatherWebMay 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 … dachshund pure and hot purifierWebOptitype 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家庭版不支持docker，要想支持得修改注册表一通操作，太麻烦了。 dachshund pyjamas for women