bcbio-nextgen.readthedocs.io

Indices and tables — bcbio-nextgen 1.0.0 documentation

Common Workflow Language (CWL). A python toolkit providing best-practice pipelines for fully automated high throughput sequencing analysis. You write a high level configuration file specifying your inputs and analysis parameters. This input drives a parallel pipeline that handles distributed execution, idempotent processing restarts and safe transactional steps. The goal is to provide a shared community resource that handles the data processing component of sequencing analysis, providing rese...

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Indices and tables — bcbio-nextgen 1.0.0 documentation | bcbio-nextgen.readthedocs.io Reviews

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Common Workflow Language (CWL). A python toolkit providing best-practice pipelines for fully automated high throughput sequencing analysis. You write a high level configuration file specifying your inputs and analysis parameters. This input drives a parallel pipeline that handles distributed execution, idempotent processing restarts and safe transactional steps. The goal is to provide a shared community resource that handles the data processing component of sequencing analysis, providing rese...

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Indices and tables — bcbio-nextgen 1.0.0 documentation | bcbio-nextgen.readthedocs.io Reviews

https://bcbio-nextgen.readthedocs.io

Common Workflow Language (CWL). A python toolkit providing best-practice pipelines for fully automated high throughput sequencing analysis. You write a high level configuration file specifying your inputs and analysis parameters. This input drives a parallel pipeline that handles distributed execution, idempotent processing restarts and safe transactional steps. The goal is to provide a shared community resource that handles the data processing component of sequencing analysis, providing rese...

INTERNAL PAGES

bcbio-nextgen.readthedocs.io

1

Introduction — bcbio-nextgen 1.0.2 documentation

http://bcbio-nextgen.readthedocs.io/en/latest/contents/introduction.html

Common Workflow Language (CWL). Bcbio-nextgen provides best-practice pipelines for automated analysis of high throughput sequencing data with the goal of being:. Quantifiable: Doing good science requires being able to accurately assess the quality of results and re-verify approaches as new algorithms and software become available. Analyzable: Results feed into tools to make it easy to query and visualize the results. Harvard School of Public Health. We use bcbio-nextgen within the bioinformatics core for...

2

Outputs — bcbio-nextgen 1.0.2 documentation

http://bcbio-nextgen.readthedocs.io/en/latest/contents/outputs.html

Common Workflow Language (CWL). Bcbio-nextgen runs in a temporary work directory which contains a number of processing intermediates. Pipeline completion extracts the final useful output files into a separate directory, specified by the Upload. This configuration allows upload to local directories, Galaxy, or Amazon S3. Once extracting and confirming the output files, you can delete the temporary directory to save space. 8211; Directory of quality control runs for the sample. These include charts and...

3

Sequencer integration — bcbio-nextgen 1.0.2 documentation

http://bcbio-nextgen.readthedocs.io/en/latest/contents/sequencer.html

Common Workflow Language (CWL). Bcbio-nextgen supports processing of samples arriving from sequencing machines. It automates the generation of de-multiplexed fastq files and sample configurations that feed directly into standard bcbio-nextgen pipelines. This requires an Illumina sequencer, and samples annotated using the basic Galaxy nglims. The approach is general and we’d be happy to collaborate or accept contributions for supporting other sequencers or LIMS systems. A front end Galaxy nglims. An analy...

4

Amazon Web Services — bcbio-nextgen 1.0.2 documentation

http://bcbio-nextgen.readthedocs.io/en/latest/contents/cloud.html

Common Workflow Language (CWL). Amazon Web Services (AWS). Provides a flexible cloud based environment for running analyses. Cloud approaches offer the ability to perform analyses at scale with no investment in local hardware. They also offer full programmatic control over the environment, allowing bcbio to automate the entire setup, run and teardown process. Provides a wrapper around bcbio-nextgen that automates interaction with AWS and Docker. With an isolated Python:. And avoid issues with resolution ...

5

Getting started — bcbio-nextgen 1.0.2 documentation

http://bcbio-nextgen.readthedocs.io/en/latest/contents/testing.html

Whole genome trio (50x). Exome with validation against reference materials. Cancer-like mixture with Genome in a Bottle samples. Structural variant calling – whole genome NA12878 (50x). Human genome build 38. Common Workflow Language (CWL). Create a sample configuration file. For your project (substitute the example BAM and fastq names below with the full path to your sample files):. Documentation has full details on available options. Run analysis, distributed across 8 local cores:. Directory has all of...

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cnvkit.readthedocs.io

CNVkit: Genome-wide copy number from targeted DNA sequencing — CNVkit 0.8.0 documentation

http://cnvkit.readthedocs.io/en/v0.8.0

Copy number calling pipeline. Text and tabular reports. Compatibility and other I/O. Calling copy number gains and losses. Whole-genome sequencing and targeted amplicon capture. Python API (cnvlib package). CNVkit: Genome-wide copy number from targeted DNA sequencing. CNVkit: Genome-wide copy number from targeted DNA sequencing. Apache License 2.0. Download the reference genome. Map sequencing reads to the reference genome. Build a reference from normal samples and infer tumor copy ratios. FAQ and How To.

cnvkit.readthedocs.io

CNVkit: Genome-wide copy number from targeted DNA sequencing — CNVkit 0.8.6.dev0 documentation

http://cnvkit.readthedocs.io/en/latest

Copy number calling pipeline. Text and tabular reports. Compatibility and other I/O. Calling copy number gains and losses. Allele frequencies and copy number. Whole-genome sequencing and targeted amplicon capture. Python API (cnvlib package). CNVkit: Genome-wide copy number from targeted DNA sequencing. CNVkit: Genome-wide copy number from targeted DNA sequencing. Apache License 2.0. Download the reference genome. Map sequencing reads to the reference genome. Copy number calling pipeline. FAQ and How To.

cnvkit.readthedocs.io

CNVkit: Genome-wide copy number from targeted DNA sequencing — CNVkit 0.8.1 documentation

http://cnvkit.readthedocs.io/en/v0.8.1

Copy number calling pipeline. Text and tabular reports. Compatibility and other I/O. Calling copy number gains and losses. Whole-genome sequencing and targeted amplicon capture. Python API (cnvlib package). CNVkit: Genome-wide copy number from targeted DNA sequencing. CNVkit: Genome-wide copy number from targeted DNA sequencing. Apache License 2.0. Download the reference genome. Map sequencing reads to the reference genome. Build a reference from normal samples and infer tumor copy ratios. FAQ and How To.

cnvkit.readthedocs.io

Quick start — CNVkit 0.8.5 documentation

http://cnvkit.readthedocs.io/en/stable/quickstart.html

Download the reference genome. Map sequencing reads to the reference genome. Build a reference from normal samples and infer tumor copy ratios. Copy number calling pipeline. Text and tabular reports. Compatibility and other I/O. Calling copy number gains and losses. Allele frequencies and copy number. Whole-genome sequencing and targeted amplicon capture. Python API (cnvlib package). If you would like to quickly try CNVkit without installing it, try our app on DNAnexus. And read the README file. We&#8217...

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bcbio-nextgen.readthedocs.io

Indices and tables — bcbio-nextgen 1.0.0 documentation

Common Workflow Language (CWL). A python toolkit providing best-practice pipelines for fully automated high throughput sequencing analysis. You write a high level configuration file specifying your inputs and analysis parameters. This input drives a parallel pipeline that handles distributed execution, idempotent processing restarts and safe transactional steps. The goal is to provide a shared community resource that handles the data processing component of sequencing analysis, providing rese...

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