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Optitype使用

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 … WebNGS-based HLA typing algorithm. Container. Pulls 10K+ Overview Tags. Dockerfile ################################################################# # Dockerfile ...

OptiType: Precision HLA typing from next-generation sequencing data

Web关于 GitLab GitLab：DevOps 平台 浏览 GitLab 安装 GitLab 定价 与专家交谈 / WebAug 20, 2014 · OptiType (v1.3.3) [37] was performed on germline pairedend whole-genome sequencing fastq files after fishing for HLA reads at 95% identity, taking only the top match with razers3 (v3.5.8) [38 ... ffwcl https://gcprop.net

OptiType on Biowulf - National Institutes of Health

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 … WebJan 18, 2024 · I tried to install optitype as follow: conda install -c bioconda optitype I got the message: Collecting package metadata (current_repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve. Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source. 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 … ffw.com

HLA-VBSeq:对全基因组数据进行HLA分型 - 腾讯云开发者社区-腾讯云

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Optitype使用

opitype:对HLA I型基因进行4位分型 - 腾讯云开发者社区-腾讯云

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。 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 …

Optitype使用

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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 … WebNov 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 ...

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 … 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

Web4.使用optitype进行分型: OptiTypePipeline.py -i input_1.fastq input_2.fastq --rna -v -o /path/to/output/dir/. 详细参数说明请参照之前的文章 生科院的老张：服务器singularity安 … 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 …

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 … density into poundsWebJul 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 … ffwct arlington majorWebNov 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. ffwcrcWeboptitype¶ 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. ffwc reddem codeWebMay 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 … ffwc olean nyhttp://www.yucebio.com/NewsInformation/Inner/419 density instrument airWeblinux-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" … density in standard units