Daily Archives: Thursday May 12th, 2022

GASystemChannel －GA09 QIIME2 微生物群集分析(coming soon) Environment requirement Hardware :    CPU : 10 cores RAM : 45 Gb Software :The pipeline is developed based on GA System. All software used in the pipeline are included in pre-defined software environments (GA application collection ). Please install suitable environment before start the pipeline(How to do it!) . The diagram of workflow Reference Microbiome Path Source Silva138NBscikit0.24.1 /staging/reserve/GAResource/GA_bundle/Ref/Microbiome/QIIME2/v2021.8/ QIIME2_Data_resources Greengenes138NBscikit0.24.1 /staging/reserve/GAResource/GA_bundle/Ref/Microbiome/QIIME2/v2021.8/ QIIME2_Data_resources RDPtraset18scikit0.24.1 /staging/reserve/GAResource/GA_bundle/Ref/Microbiome/QIIME2/v2021.8/RDPclassifier/ RDP Classifier NCBIBioProj33175scikit0.24.1 /staging/reserve/GAResource/GA_bundle/Ref/Microbiome/QIIME2/v2021.8/NCBIclassifier/BioProject_33175/ QIIME2_forum NCBIBioProj33317scikit0.24.1 /staging/reserve/GAResource/GA_bundle/Ref/Microbiome/QIIME2/v2021.8/NCBIclassifier/BioProject_33317/ QIIME2_forum

GA09 QIIME2 微生物群集分析

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GASystemChannel －GA07 DESeq表現量差異分析 (coming soon) Environment requirement Hardware :CPU : 10 coresRAM : 45G Software :The pipeline is developed based on GA System. All software used in the pipeline are included in pre-defined software environments (GA application collection ). Please install suitable environment before start the pipeline(How to do it!) . The diagram of workflow Reference Homo_sapiens Path Source GRCh38en94Star2.7.5a Archive GRCh38 Release 94 GRCh38en102Star2.7.5a Archive GRCh38 Release 102 GRCh38en104Star2.7.5a /staging/reserve/GAResource/GA_bundle/Ref/Homo_sapiens/GRCh38en104Star2.7.5a GRCh38 Release 104 Mus_musculus Path Source GRCm38en101Star2.7.5a Archive GRCm38 Release 101 GRCm39en104Star2.7.5a /staging/reserve/GAResource/GA_bundle/Ref/Mus_musculus/GRCm39en104Star2.7.5a GRCm39 Release 104

GA07 DESeq表現量差異分析

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Background 在定序技術中，特別是次世代定序(NGS)，近年常被廣泛用在臨床應用，特別是非侵入性孕前檢測(Bianchi et al., 2015) 及癌症檢測。而序列樣品可能因為轉接子(Adapter)汙染、鹼基序列的誤差，或過度表現的片段造成分析的困難。更甚者，可能還會因為製備序列資料庫(Library)及定序過程的錯誤，造成不正確的核酸定序結果。因此，為了取得良好品質及高可信度的序列樣品以進行分析，序列品質控管及前處理為非常重要的一個環節。 Environment requirement Hardware: CPU : 2 cores RAM : 8 Gb Software :The pipeline is developed based on GA System. All software used in the pipeline are included in pre-defined software environments (GA application collection ). Please install suitable environment before start the pipeline(How to do it!) . The diagram of workflow GASystemChannel －GA02 序列檔案品質分析 (coming soon) Demo_code: download　　

GA02 序列檔案品質分析

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GASystemChannel －GA08 SNPEff & dbNSFP基因註解析 (coming soon) Environment requirement Hardware :    CPU : 10 cores RAM : 45 Gb Software :The pipeline is developed based on GA System. All software used in the pipeline are included in pre-defined software environments (GA application collection ). Please install suitable environment before start the pipeline(How to do it!) . The diagram of workflow Reference For GATK Homo_sapiens Path Source GATK_b37  /work/opt/ohpc/Taiwania3/pkg/biology/reference/Homo_sapiens/GATK/b37 GATK_Resource_bundle GATK_hg19 /work/opt/ohpc/Taiwania3/pkg/biology/reference/Homo_sapiens/GATK/hg19 GATK_Resource_bundle GATK_hg38  /work/opt/ohpc/Taiwania3/pkg/biology/reference/Homo_sapiens/GATK/hg38 GATK_Resource_bundle GATK_Mutect2 /work/opt/ohpc/Taiwania3/pkg/biology/reference/Homo_sapiens/GATK/Mutect2 GATK_Mutect2 For annovar Homo_sapiens Path Source ANNOVAR_hg19 /work/opt/ohpc/Taiwania3/pkg/biology/reference/Homo_sapiens/annovar/hg19 Annovar ANNOVAR_hg38 /work/opt/ohpc/Taiwania3/pkg/biology/reference/Homo_sapiens/annovar/hg38 Annovar For SnpEff SnpEff_GRCh37.87 /work/opt/ohpc/Taiwania3/pkg/biology/SnpEff/snpEff_v5.0e/data/GRCh37.87 SnpEff SnpEff_GRCh38.99 /work/opt/ohpc/Taiwania3/pkg/biology/SnpEff/snpEff_v5.0e/data/GRCh38.99 SnpEff SnpEff_GRCm38.99 /work/opt/ohpc/Taiwania3/pkg/biology/SnpEff/snpEff_v5.0e/data/GRCm38.99 SnpEff For SnpSift dbNSFP4.1a /work/opt/ohpc/Taiwania3/pkg/biology/SnpEff/snpEff_v5.0e/data/ SnpSift

GA08 SNPEff & dbNSFP基因註解析

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GASystemChannel －GA06 GATK-體變異點分析(Somatic) (coming soon) Environment requirement Hardware :    CPU : 10 cores RAM : 45 Gb Software :The pipeline is developed based on GA System. All software used in the pipeline are included in pre-defined software environments (GA application collection ). Please install suitable environment before start the pipeline(How to do it!) . The diagram of workflow Reference For GATK Homo_sapiens Path Source GATK_b37  /work/opt/ohpc/Taiwania3/pkg/biology/reference/Homo_sapiens/GATK/b37 GATK_Resource_bundle GATK_hg19 /work/opt/ohpc/Taiwania3/pkg/biology/reference/Homo_sapiens/GATK/hg19 GATK_Resource_bundle GATK_hg38  /work/opt/ohpc/Taiwania3/pkg/biology/reference/Homo_sapiens/GATK/hg38 GATK_Resource_bundle GATK_Mutect2 /work/opt/ohpc/Taiwania3/pkg/biology/reference/Homo_sapiens/GATK/Mutect2 GATK_Mutect2 For annovar Homo_sapiens Path Source ANNOVAR_hg19 /work/opt/ohpc/Taiwania3/pkg/biology/reference/Homo_sapiens/annovar/hg19 Annovar ANNOVAR_hg38 /work/opt/ohpc/Taiwania3/pkg/biology/reference/Homo_sapiens/annovar/hg38 Annovar For SnpEff SnpEff_GRCh37.87 /work/opt/ohpc/Taiwania3/pkg/biology/SnpEff/snpEff_v5.0e/data/GRCh37.87 SnpEff SnpEff_GRCh38.99 /work/opt/ohpc/Taiwania3/pkg/biology/SnpEff/snpEff_v5.0e/data/GRCh38.99 SnpEff SnpEff_GRCm38.99 /work/opt/ohpc/Taiwania3/pkg/biology/SnpEff/snpEff_v5.0e/data/GRCm38.99 SnpEff For SnpSift dbNSFP4.1a /work/opt/ohpc/Taiwania3/pkg/biology/SnpEff/snpEff_v5.0e/data/ SnpSift

GA06 GATK-體變異點分析(Somatic)

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GASystemChannel －GA05 GATK-遺傳變異點分析(Germline) (coming soon) Environment requirement Hardware :    CPU : 10 cores RAM : 45 Gb Software :The pipeline is developed based on GA System. All software used in the pipeline are included in pre-defined software environments (GA application collection ). Please install suitable environment before start the pipeline(How to do it!) . The diagram of workflow Reference For GATK Homo_sapiens Path Source GATK_b37  /work/opt/ohpc/Taiwania3/pkg/biology/reference/Homo_sapiens/GATK/b37 GATK_Resource_bundle GATK_hg19 /work/opt/ohpc/Taiwania3/pkg/biology/reference/Homo_sapiens/GATK/hg19 GATK_Resource_bundle GATK_hg38  /work/opt/ohpc/Taiwania3/pkg/biology/reference/Homo_sapiens/GATK/hg38 GATK_Resource_bundle GATK_Mutect2 /work/opt/ohpc/Taiwania3/pkg/biology/reference/Homo_sapiens/GATK/Mutect2 GATK_Mutect2 For annovar Homo_sapiens Path Source ANNOVAR_hg19 /work/opt/ohpc/Taiwania3/pkg/biology/reference/Homo_sapiens/annovar/hg19 Annovar ANNOVAR_hg38 /work/opt/ohpc/Taiwania3/pkg/biology/reference/Homo_sapiens/annovar/hg38 Annovar

GA05 GATK-遺傳變異點分析(Germline)

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GASystemChannel －GA04 GATK-序列比對 (coming soon) Environment requirement Hardware :    CPU : 10 cores RAM : 45 Gb Software :The pipeline is developed based on GA System. All software used in the pipeline are included in pre-defined software environments (GA application collection ). Please install suitable environment before start the pipeline(How to do it!) . The diagram of workflow Reference For GATK Homo_sapiens Path Source GATK_b37  /work/opt/ohpc/Taiwania3/pkg/biology/reference/Homo_sapiens/GATK/b37 GATK_Resource_bundle GATK_hg19 /work/opt/ohpc/Taiwania3/pkg/biology/reference/Homo_sapiens/GATK/hg19 GATK_Resource_bundle GATK_hg38  /work/opt/ohpc/Taiwania3/pkg/biology/reference/Homo_sapiens/GATK/hg38 GATK_Resource_bundle GATK_Mutect2 /work/opt/ohpc/Taiwania3/pkg/biology/reference/Homo_sapiens/GATK/Mutect2 GATK_Mutect2 For annovar Homo_sapiens Path Source ANNOVAR_hg19 /work/opt/ohpc/Taiwania3/pkg/biology/reference/Homo_sapiens/annovar/hg19 Annovar ANNOVAR_hg38 /work/opt/ohpc/Taiwania3/pkg/biology/reference/Homo_sapiens/annovar/hg38 Annovar For SnpEff SnpEff_GRCh37.87 /work/opt/ohpc/Taiwania3/pkg/biology/SnpEff/snpEff_v5.0e/data/GRCh37.87 SnpEff SnpEff_GRCh38.99 /work/opt/ohpc/Taiwania3/pkg/biology/SnpEff/snpEff_v5.0e/data/GRCh38.99 SnpEff SnpEff_GRCm38.99 /work/opt/ohpc/Taiwania3/pkg/biology/SnpEff/snpEff_v5.0e/data/GRCm38.99 SnpEff For SnpSift dbNSFP4.1a /work/opt/ohpc/Taiwania3/pkg/biology/SnpEff/snpEff_v5.0e/data/ SnpSift

GA04 GATK-序列比對(mapping)

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GASystemChannel －GA03 基因表現量分析 (coming soon) Demo_code : download Environment requirement Hardware :CPU : 10 coresRAM : 45G Software :The pipeline is developed based on GA System. All software used in the pipeline are included in pre-defined software environments (GA application collection ). Please install suitable environment before start the pipeline(How to do it!) . The diagram of workflow Reference Homo_sapiens Path Source GRCh38en94Star2.7.5a Archive GRCh38 Release 94 GRCh38en102Star2.7.5a Archive GRCh38 Release 102 GRCh38en104Star2.7.5a /staging/reserve/GAResource/GA_bundle/Ref/Homo_sapiens/GRCh38en104Star2.7.5a GRCh38 Release 104 Mus_musculus Path Source GRCm38en101Star2.7.5a Archive GRCm38 Release 101 GRCm39en104Star2.7.5a /staging/reserve/GAResource/GA_bundle/Ref/Mus_musculus/GRCm39en104Star2.7.5a GRCm39 Release 104

GA03 RNAseq_基因表現量分析:

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