Fred2/optitype
WebParameters: ngsFile (str) – The path to the NGS file of interest; output (str) – The path to the output file or directory; command (str) – The path to a alternative binary (if binary is not globally executable); options (str) – A string with additional options that is directly past to the tool; delete (bool) – Boolean indicator whether generated files should be deleted afterwards WebJan 1, 2016 · FRED 2 (framework for epitope detection) is an opensource framework designed to address the issue of the large number of pipelines and tools that each require unique inputs and provide different...
Fred2/optitype
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WebOptiType/OptiTypePipeline.py. from NGS data by simultaneously selecting all minor and major HLA-I alleles. and their dependencies. in the configuration file for RazerS 3.1. CPLEX should be globally executable. … WebOct 7, 2024 · Genetic instability of tumors leads to the appearance of numerous tumor-specific somatic mutations that could potentially result in the production of mutated peptides that are presented on the cell surface by the MHC molecules. Peptides of this kind are commonly called neoantigens. Their presence on the cell surface specifically …
WebApr 14, 2024 · 接下来要修改Optitype文件夹里的config.ini文件。. 复制一个example来修改即可（其实除了razers的路径和线程数，没啥好改的，glpk只能单线程运行，修改线程数没用）。. Optitype会调用razers进行比对。. cp config.ini.example config.ini. 软件的运行. python OptiTypePipeline.py \ -i sample ... WebHi @207261kaceamatr (顧客) . You are just using the wrong option description. Read the manual carefully to understand how to use the options. [Note] "(-r -d)" means that the -r or -d option is present as an optional option.
WebDec 19, 2024 · I did the following and so far optitype is running: sudo adduser biodocker sudo chown -R :users /work/Projects sudo chmod -R 777 /work/Projects sudo docker run -v /work/Projects:/data -t fred2/optitype -i EA005_001_1.fq EA005_001_2.fq -d -o /data http://fred-2.github.io/getting-started/
WebJun 25, 2014 · For Advanced Users and Developers. Databases - This tutorial familiarizes the advanced users with internal functionalities of FRED2’s data base adapters. …
WebDec 1, 2014 · OptiType: precision HLA typing from next-generation sequencing data Bioinformatics. 2014 Dec 1;30 (23):3310-6. doi: 10.1093/bioinformatics/btu548. Epub 2014 Aug 20. Authors András Szolek 1 , Benjamin Schubert 2 , Christopher Mohr 2 , Marc Sturm 1 , Magdalena Feldhahn 1 , Oliver Kohlbacher 1 Affiliations heather donahue always sunnyWebFeb 17, 2024 · I tried bootstrapping the singularity image as follows: singularity build optitype.simg docker://fred2/optitype However, this does not seem to run as expected. … movie a woman\u0027s face 1941WebParameters: ngsFile (str) – The path to the NGS file of interest; output (str) – The path to the output file or directory; command (str) – The path to a alternative binary (if binary is … movie a window in londonWebOptiType 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. References: OptiType: precision HLA typing from next-generation sequencing data. movie a wedding to rememberWebFeb 17, 2024 · I tried bootstrapping the singularity image as follows: singularity build optitype.simg docker://fred2/optitype However, this does not seem to run as expected. Could someone with experience bootstrapping docker files onto singularity suggest how I ~ Optitype for Singularity movie a white white dayWebOptitype. Describes dependencies and installation of optitype, used in this course for HLA typing # due to the complexity of optitype dependencies we will use a docker image for optitype # pull docker image as ubuntu user … heather donahue bookWebApr 13, 2024 · Although chemotherapy plus PD-1 blockade (chemo+anti-PD-1) has become the standard first-line therapy for advanced esophageal squamous cell carcinoma … movie a winter princess