l3sdk.l3-bioinfo.com

Welcome to L3 BGI-Online SDK’s documentation! — L3 BGI Online SDK beta documentation

L3 BGI Online SDK. Example: 3K Rice Genome Project. Example: BWA GATK (Alpha, Obseleted). Example: TopHat (Alpha, Obseleted). Welcome to L3 BGI-Online SDK’s documentation! Welcome to L3 BGI-Online SDK’s documentation! The L3 BGI Online SDK is a Python library and a command-line tool that makes it easy to port bioinformatics pipelines to BGI Online cloud platform. The L3 BGI Online SDK was developed based on the open-source software SBGSDK. Whose tutorial can be found here. Initializing a new tool project.

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Welcome to L3 BGI-Online SDK’s documentation! — L3 BGI Online SDK beta documentation | l3sdk.l3-bioinfo.com Reviews

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L3 BGI Online SDK. Example: 3K Rice Genome Project. Example: BWA GATK (Alpha, Obseleted). Example: TopHat (Alpha, Obseleted). Welcome to L3 BGI-Online SDK’s documentation! Welcome to L3 BGI-Online SDK’s documentation! The L3 BGI Online SDK is a Python library and a command-line tool that makes it easy to port bioinformatics pipelines to BGI Online cloud platform. The L3 BGI Online SDK was developed based on the open-source software SBGSDK. Whose tutorial can be found here. Initializing a new tool project.

<META> KEYWORDS

1 site map

2 wrapping tutorial

3 quick jump

4 note

5 contents

6 obtaining the sdk

7 metadata

8 resource requirements

9 wrapping big tools

10 naming convention

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Welcome to L3 BGI-Online SDK’s documentation! — L3 BGI Online SDK beta documentation | l3sdk.l3-bioinfo.com Reviews

https://l3sdk.l3-bioinfo.com

L3 BGI Online SDK. Example: 3K Rice Genome Project. Example: BWA GATK (Alpha, Obseleted). Example: TopHat (Alpha, Obseleted). Welcome to L3 BGI-Online SDK’s documentation! Welcome to L3 BGI-Online SDK’s documentation! The L3 BGI Online SDK is a Python library and a command-line tool that makes it easy to port bioinformatics pipelines to BGI Online cloud platform. The L3 BGI Online SDK was developed based on the open-source software SBGSDK. Whose tutorial can be found here. Initializing a new tool project.

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l3sdk.l3-bioinfo.com

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Example: TopHat (Alpha, Obseleted) — L3 BGI Online SDK beta documentation

http://l3sdk.l3-bioinfo.com/example_tophat.html

L3 BGI Online SDK. Example: 3K Rice Genome Project. Example: BWA GATK (Alpha, Obseleted). Example: TopHat (Alpha, Obseleted). Example: TopHat (Alpha, Obseleted). Example: TopHat (Alpha, Obseleted). Install TopHat in the docker container. Apt-get update apt-get install tophat. In the docker container:. Opt/ `- db - hg19.1.bt2 - hg19.2.bt2 - hg19.3.bt2 - hg19.4.bt2 - hg19.fa - hg19.rev.1.bt2 - hg19.rev.2.bt2 - hg19.zip `- make hg19.sh. Supply TopHat with a list of deletions with respect to the reference.

2

Wrapping Tutorial — L3 BGI Online SDK beta documentation

http://l3sdk.l3-bioinfo.com/tutorial.html

L3 BGI Online SDK. Example: 3K Rice Genome Project. Example: BWA GATK (Alpha, Obseleted). Example: TopHat (Alpha, Obseleted). Initializing a new tool project. Creating the Docker image. Writing the wrapper class. Running the wrapper locally. Uploading the tool to BGI Online. Before you can run your own tool on the BGI Online platform, it must be first. The L3 BGI Online SDK was developed based on the open-source software SBGSDK. Whose tutorial can be found here. After installing, download this archive.

3

Example: 3K Rice Genome Project — L3 BGI Online SDK beta documentation

http://l3sdk.l3-bioinfo.com/example_ricegenome.html

L3 BGI Online SDK. Example: 3K Rice Genome Project. Example: BWA GATK (Alpha, Obseleted). Example: TopHat (Alpha, Obseleted). Example: 3K Rice Genome Project. Example: 3K Rice Genome Project. With the rapid and ever-increasing growth of genomic data, it has become a real challenge how to manage such data while enabling efficient derivation of useful information. BGI-Online is a time-and-cost efficient solution to meet this challenge. The 3K Rice Genomes Project [1]. Input Short Read Archinve (SRA) file.

4

Example: BWA+GATK (Alpha, Obseleted) — L3 BGI Online SDK beta documentation

http://l3sdk.l3-bioinfo.com/example_bwagatk.html

L3 BGI Online SDK. Example: 3K Rice Genome Project. Example: BWA GATK (Alpha, Obseleted). Example: TopHat (Alpha, Obseleted). Example: BWA GATK (Alpha, Obseleted). Tool: GATK SelectVariant (SNP). Tool: GATK SelectVariant (INDEL). Tool: SNP Filter Perl Script. Tool: Indel Filter Perl Script. Corresponding Pipeline in a Perl Script. Example: BWA GATK (Alpha, Obseleted). Input a pair of FASTQ file. In the docker container:. In the docker container:. Please input fq1 fq2 and sampleName n. S ) 1 .fq/. Dedup r...

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bgionline.com

BGI Online

https://www.bgionline.com/case02.html

Use Cases Diagnostic Test Providers. Feeding data from the sequencing machines to analysis pipelines, and then delivering the results to clients can take months with traditional infrastructure. BGI Online automates these tasks through integration with your current Laboratory Information Management Systems (LIMS) and decreases the time spent on logistics. You can now focus on bringing more value to your customers while increasing your own revenues. Security every step of the way. Read security white paper.

bgionline.com

BGI Online

https://www.bgionline.com/pipeline.html

WES Human Whole Exome Sequencing Analysis Pipeline (BGI Refined). WGS Human Whole Genome Sequencing Analysis Pipeline (BGI Refined). RNA-seq : RNA-seq Analysis Pipeline (BGI Refined). Whole Genome Analysis 30x - BWA GATK. Whole Exome Analysis - BWA GATK 2.3.9-Lite (with Metrics) (General). Whole Genome Analysis - BWA GATK 2.3.9-Lite (with Metrics) (General). RNA-Seq Differential Expression - Cuffdiff (with Visualization) (General). 50x coverage WGS (150GB): 4 hours. 200x coverage WES (10G): 15 mins.

bgionline.com

BGI Online

https://www.bgionline.com/index.html

Analyse, store and share. Your genomics data securely. BGI Online helps you on genome sequencing and analysis projects, while eliminating software setup and file transfer logistics. It is a secure cloud platform for bioinformaticians to advance life-saving research. Access the world’s largest. Repository of genomic data. Use our best practices or create your own pipeline. Share your findings to clients and peers. Visualise your results using database.bio. Who can use BGI Online? 8226; Tool developers.

bgionline.com

BGI Online

https://www.bgionline.com/case03.html

Use Cases Biopharmaceutical Company. Analysis performed by research and development teams is valuable proprietary knowledge. But managing such information across large teams is difficult. With BGI Online’s ability to customise project permissions by granting specific access to individuals, team members can now focus on discovering the next medical breakthrough. Integrate seamlessly and increase your revenues. Security every step of the way. Read security white paper. Easily share your results. Main Build...

bgionline.com

BGI Online

https://www.bgionline.com/case01.html

Use Cases Sequencing Providers. Data generated by sequencing genomes take up petabytes of storage space. The cost of infrastructure upgrade and storage capacity limits the range of services that can be provided. With BGI Online’s cloud computing, you can expand your service portfolio without further investments and focus on delivering value to clients. Expand service offerings without more investment. Security every step of the way. Read security white paper. Easily share your results. Main Building, Bei...

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Welcome to L3 BGI-Online SDK’s documentation! — L3 BGI Online SDK beta documentation

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