二級分析 工具集 === ###### tags: `基因體/二級分析` ###### tags: `生物資訊`, `基因體`, `二級分析`, `tools` <br> [TOC] <br> ## WGS / WES Pipeline > 全基因體定序 / 全外顯子定序 分析流程 > - [簡介什麼是全外顯子定序(whole exome sequence, WES)及其應用](https://unclegene6666.pixnet.net/blog/post/351067985) > ### GPU Based - ### Tools | Category | Tool | | -------- | ---- | | FASTQ/BAM Processing | [applybqsr](https://docs.nvidia.com/clara/parabricks/4.0.0/Documentation/ToolDocs/man_applybqsr.html#man-applybqsr)<br>[bam2fq](https://docs.nvidia.com/clara/parabricks/4.0.0/Documentation/ToolDocs/man_bam2fq.html#man-bam2fq)<br>[bamsort](https://docs.nvidia.com/clara/parabricks/4.0.0/Documentation/ToolDocs/man_bamsort.html#man-bamsort)<br>[bqsr](https://docs.nvidia.com/clara/parabricks/4.0.0/Documentation/ToolDocs/man_bqsr.html#man-bqsr)<br>[fq2bam](https://docs.nvidia.com/clara/parabricks/4.0.0/Documentation/ToolDocs/man_fq2bam.html#man-fq2bam) | | Quality Control | [bammetrics](https://docs.nvidia.com/clara/parabricks/4.0.0/Documentation/ToolDocs/man_bammetrics.html#man-bammetrics)<br>[collectmultiplemetrics](https://docs.nvidia.com/clara/parabricks/4.0.0/Documentation/ToolDocs/man_collectmultiplemetrics.html#man-collectmultiplemetrics) | | Variant Calling | [deepvariant](https://docs.nvidia.com/clara/parabricks/4.0.0/Documentation/ToolDocs/man_deepvariant.html#man-deepvariant)<br>[haplotypecaller](https://docs.nvidia.com/clara/parabricks/4.0.0/Documentation/ToolDocs/man_haplotypecaller.html#man-haplotypecaller) | | GVCF Processing | [indexgvcf]()<br>[genotypegvcf](https://docs.nvidia.com/clara/parabricks/4.0.0/Documentation/ToolDocs/man_genotypegvcf.html#man-genotypegvcf) | | Variant Processing | [dbsnp](https://docs.nvidia.com/clara/parabricks/4.0.0/Documentation/ToolDocs/man_dbsnp.html#man-dbsnp) | | Pipelines | [deepvariant_germline](https://docs.nvidia.com/clara/parabricks/4.0.0/Documentation/ToolDocs/man_deepvariant_germline.html#man-deepvariant-germline)<br>[germline](https://docs.nvidia.com/clara/parabricks/4.0.0/Documentation/ToolDocs/man_germline.html#man-germline) | - ### [germline](https://docs.nvidia.com/clara/parabricks/4.0.0/Documentation/ToolDocs/man_germline.html) [![](https://i.imgur.com/TnuHVlV.png)](https://docs.nvidia.com/clara/parabricks/4.0.0/_images/germline.png) - ### [deepvariant_germline](https://docs.nvidia.com/clara/parabricks/4.0.0/Documentation/ToolDocs/man_deepvariant_germline.html) [![](https://i.imgur.com/233Zx9R.png)](https://docs.nvidia.com/clara/parabricks/4.0.0/_images/deep_variant.png) <br> ### CPU Based - Tools | Tool | Version | Official | | ---------------- | ------- | -------- | | [FastQC](https://github.com/s-andrews/FastQC) | 0.11.9 | [doc](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) | | [MultiQC](https://github.com/ewels/MultiQC) | 1.13 | [doc](https://multiqc.info/) | | [bwa](https://github.com/lh3/bwa) | 0.7.15 | [doc](https://bio-bwa.sourceforge.net/) | | [GATK](https://github.com/broadinstitute/gatk) | 4.1.0.0, 4.2.0.0 | [doc](https://gatk.broadinstitute.org/hc/en-us/articles/10082764643867--GATK-4-3-release) | | [TrimGalore](https://github.com/FelixKrueger/TrimGalore) | 0.6.7 | [doc](https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) | - ### [Pipeline summary - single samples](https://github.com/ESR-NZ/human_genomics_pipeline#pipeline-summary---single-samples) ![](https://i.imgur.com/5lpds8i.png) <br> <hr> <hr> <br> ## Environment Software | Tool | Version | Official | | ---------------- | ------- | -------- | | [python](https://github.com/python) | * | [doc](https://www.python.org/) | | [conda](https://github.com/conda/conda) | * | [doc](https://docs.conda.io/en/latest/) | | [mamba](https://github.com/mamba-org/mamba) | * | [doc](https://mamba.readthedocs.io/en/latest/) | | [gsutil](https://github.com/GoogleCloudPlatform/gsutil) | 5.17 | [doc](https://github.com/GoogleCloudPlatform/gsutil) | | [sratoolkit](https://github.com/ncbi/sra-tools) | 3.0.1 | [doc](https://www.ncbi.nlm.nih.gov/sra) | <br> ## CPU Software | Tool | Version | Official | | ---------------- | ------- | -------- | | [arriba](https://github.com/suhrig/arriba) | 2.1.0 | | [bcftools](https://github.com/samtools/bcftools) | 1.10.2 | [doc](https://samtools.github.io/bcftools/howtos/install.html) | | [bwa](https://github.com/lh3/bwa) | 0.7.15 | [doc](https://bio-bwa.sourceforge.net/) | | [cnvkit](https://github.com/etal/cnvkit) | 0.9.7 | [doc](https://cnvkit.readthedocs.io/en/stable/) | [Deepvariant](https://github.com/google/deepvariant) | 1.0, 1.1, 1.4 | | [Expansion Hunter](https://github.com/Illumina/ExpansionHunter) | 5.0.0 | | [FastQC](https://github.com/s-andrews/FastQC) | 0.11.9 | [doc](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) | | [fgbio](https://github.com/fulcrumgenomics/fgbio) | 1.4.0 | [doc](http://fulcrumgenomics.github.io/fgbio/) | | [GATK](https://github.com/broadinstitute/gatk) | 4.1.0.0, 4.2.0.0 | [doc](https://gatk.broadinstitute.org/hc/en-us/articles/10082764643867--GATK-4-3-release) | | [glnexus](https://github.com/dnanexus-rnd/GLnexus) | 1.2.7 | | [Kallisto](https://github.com/pachterlab/kallisto) | 0.46.2 | [doc](https://pachterlab.github.io/kallisto/) | | [lofreq](https://github.com/CSB5/lofreq) | 2.1.5 | [doc](https://csb5.github.io/lofreq/2020/06/15/lofreq-2.1.5-published-heisenbug-fixed/) | | [manta](https://github.com/Illumina/manta) | 1.6.0 | | [MultiQC](https://github.com/ewels/MultiQC) | 1.13 | [doc](https://multiqc.info/) | | [samtools](https://github.com/samtools/samtools) | 1.10 | [doc](https://www.htslib.org/) | | [somaticsniper](https://github.com/genome/somatic-sniper) | 1.0.5.0 | | [STAR](https://github.com/alexdobin/STAR) | 2.7.2a | | [STAR-Fusion](https://github.com/STAR-Fusion/STAR-Fusion) | 1.7.0 | | [strelka](https://github.com/Illumina/strelka) | 2.9.0 | | [TrimGalore](https://github.com/FelixKrueger/TrimGalore) | 0.6.7 | [doc](https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) | <br> ## GPU Software - Parabricks - ### [v4.0](https://docs.nvidia.com/clara/parabricks/4.0.0/SoftwareOverview.html) [![](https://i.imgur.com/QRqa3Il.png)](https://docs.nvidia.com/clara/parabricks/4.0.0/_images/pb_tools_v4.0.png) - [**Pipelines**](https://docs.nvidia.com/clara/parabricks/4.0.0/Documentation/ToolDocs/PipelineTools.html#pipeline-tools) - [deepvariant_germline](https://docs.nvidia.com/clara/parabricks/4.0.0/Documentation/ToolDocs/man_deepvariant_germline.html) - [germline](https://docs.nvidia.com/clara/parabricks/4.0.0/Documentation/ToolDocs/man_germline.html) - [somatic](https://docs.nvidia.com/clara/parabricks/4.0.0/Documentation/ToolDocs/man_somatic.html) - [**CPU Software**](https://docs.nvidia.com/clara/parabricks/4.0.0/Documentation/ToolDocs/CompatibleCpuSoftwareVersions.html) - ### [v3.8](https://docs.nvidia.com/clara/parabricks/3.8.0/SoftwareOverview.html) [![](https://i.imgur.com/Pgo6ARS.png)](https://docs.nvidia.com/clara/parabricks/3.8.0/_images/pb_tools_v37.png) - [**Pipelines**](https://docs.nvidia.com/clara/parabricks/3.8.0/SoftwareOverview.html#pipelines) - [deepvariant_germline](https://docs.nvidia.com/clara/parabricks/3.8.0/Documentation/ToolDocs/man_deepvariant_germline.html) - [denovomutation](https://docs.nvidia.com/clara/parabricks/3.8.0/Documentation/ToolDocs/man_denovomutation.html) - [germline](https://docs.nvidia.com/clara/parabricks/3.8.0/Documentation/ToolDocs/man_germline.html) - [human_par](https://docs.nvidia.com/clara/parabricks/3.8.0/Documentation/ToolDocs/man_human_par.html) - [rna_gatk](https://docs.nvidia.com/clara/parabricks/3.8.0/Documentation/ToolDocs/man_rna_gatk.html) - [somatic](https://docs.nvidia.com/clara/parabricks/3.8.0/Documentation/ToolDocs/man_somatic.html) - [**CPU Software**](https://docs.nvidia.com/clara/parabricks/3.8.0/SoftwareOverview.html#compatible-cpu-software-versions) - ### [v3.6.1](https://docs.nvidia.com/clara/parabricks/v3.6.1/text/software_overview.html#software-overview) [![](https://i.imgur.com/ZBQ6Dw6.png)](https://docs.nvidia.com/clara/parabricks/v3.6.1/_images/pb_pipelines.png) - [**Pipelines**](https://docs.nvidia.com/clara/parabricks/v3.6.1/text/software_overview.html#pipelines-overview) - [GERMLINE PIPELINE](https://docs.nvidia.com/clara/parabricks/v3.6.1/text/germline_pipeline.html) - [DEEPVARIANT GERMLINE PIPELINE](https://docs.nvidia.com/clara/parabricks/v3.6.1/text/deep_pipeline.html) - [HUMAN_PAR PIPELINE](https://docs.nvidia.com/clara/parabricks/v3.6.1/text/human_par_pipeline.html) - [SOMATIC PIPELINE](https://docs.nvidia.com/clara/parabricks/v3.6.1/text/somatic_pipeline.html) - [RNA PIPELINE](https://docs.nvidia.com/clara/parabricks/v3.6.1/text/rna_pipeline.html) - [Denovo PIPELINE](https://docs.nvidia.com/clara/parabricks/v3.6.1/text/denovo_pipeline.html) (new) - [**CPU Software**](https://docs.nvidia.com/clara/parabricks/v3.6.1/text/software_overview.html#compatible-cpu-software-versions) - ### [v3.5](https://docs.nvidia.com/clara/parabricks/v3.5/text/software_overview.html#software-overview) [![](https://i.imgur.com/l3NX0wh.png)](https://docs.nvidia.com/clara/parabricks/v3.5/_images/pb_pipelines.png) - [**Pipelines**](https://docs.nvidia.com/clara/parabricks/v3.5/text/software_overview.html#pipelines-overview) - [GERMLINE PIPELINE](https://docs.nvidia.com/clara/parabricks/v3.5/text/germline_pipeline.html) - [DEEPVARIANT GERMLINE PIPELINE](https://docs.nvidia.com/clara/parabricks/v3.5/text/deep_pipeline.html) - [HUMAN_PAR PIPELINE](https://docs.nvidia.com/clara/parabricks/v3.5/text/human_par_pipeline.html) - [SOMATIC PIPELINE](https://docs.nvidia.com/clara/parabricks/v3.5/text/somatic_pipeline.html) - [RNA PIPELINE](https://docs.nvidia.com/clara/parabricks/v3.5/text/rna_pipeline.html) - [**CPU Software**](https://docs.nvidia.com/clara/parabricks/v3.5/text/software_overview.html#compatible-cpu-software-versions) <br> <hr> <br> ## 參考資料 - [NVIDIA Clara Documentation](https://docs.nvidia.com/clara/) - [human_genomics_pipeline](https://github.com/ESR-NZ/human_genomics_pipeline)