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FRED-2/OptiType is licensed under the BSD 3-Clause "New" or "Revised" LicenseA permissive license similar to the BSD 2-Clause License, but with a 3rd clause that prohibits others from using the name of the copyright holder or its contributors to promote derived products without written ...
全局变量的使用示例 3.从optitype的GitHub网页获取比对需要的reference. 在optitype的GitHub链接FRED-2/OptiType找到软件提供的razers3比对所需要的reference(WGS为hla_reference_dna.fasta, RNA-Seq为hla_reference_rna.fasta),将它们下载到服务器并连同前面下载的optitype.sif一同将其所在路径添加到全局变量。(方法同上) ...
截止2022年2月看到github上的版本:2020年9月更新到了v1.3.5 image.png 安装: mkdir OptiType cd OptiType tar -zxvf OptiType-1.3.5.tar.gz image.png 可以分析dna数据(WES,WGS),也可以分析RNA数据(RNAseq),用--dna和--rna参数区分。 输入为:fastq格式: 作者建议三步走: 1,使用razers3 比对原始数据(fast...
OptiType是一款基于整数线性规划的新型HLA基因分型算法。它能从NGS(下一代测序)数据中准确预测4位数HLA基因分型。简单来说,就是它能帮你从海量的测序数据中,精准地找出你的HLA基因型。 功能特点 1.高准确性:OptiType能够从NGS数据中准确预测HLA-A、HLA-B和HLA-C三种类型的基因型,尤其对于HLA-Ia类型的准确性更...
1.https://github.com/FRED-2/OptiType 2.Szolek, A, Schubert, B, Mohr, C, Sturm, M, Feldhahn, M, and Kohlbacher, O (2014). OptiType: precision HLA typing from next-generation sequencing data Bioinformatics, 30(23):3310-6. 3.https://stackoverflow.com/questions/25980018/importerror-hdfst...
wget https://github.com/SyntekabioTools/HLAscan/releases/download/v2.0.0/dataset.zip #解压 unzip dataset.zip #循环运行分型数据 for gene in 'HLA-A HLA-B HLA-C HLA-E HLA-F HLA-G MICA MICB HLA-DMA HLA-DMB HLA-DOA HLA-DOB HLA-DPA1 HLA-DPB1 HLA-DQA1 HLA-DQB1 HLA-DRA HLA-DRB1...
P36-T.winners.hla.nofreq.txt P36-T_T_WES_P36-T_result.tsv P36.intgration.hla.txt README.md Description This tool is used to integrate the typing results of OptiType and Polysolver Function Although OptiType has high typing accuracy for control samples, however, when we used the OptiType...