batch upload pipeline - goseqit
TRANSCRIPT
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Workshop on Whole Genome Sequencing and Analysis, 19-21 Sep. 2016
The Bacterial Analysis Pipeline and batch upload
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Learning objective:
After this lecture and exercise, you should be able to…
…upload batches of data to the CGE Bacterial Analysis Pipeline, browse the results, and re-run with changed settings for individual services.
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* Assembly
* Species/Lineage prediction
* Multilocus Sequence Typing
* Resistance Gene Identification
* Plasmid Identification
* Plasmid MLST
* Virulence Gene Identification
Service Overview
Bacterial Analysis Pipeline
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Introducing the pipeline1. Input sequence file(s) and
metadata
2. Create DB entry
3. Run pipeline of services
4. Create analysis report and
update DB entry
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1. Create a user account and login
https://cge.cbs.dtu.dk/services/
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2. Download and fill out metadata sheet
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The Excel file has two sheets:
1: Empty table into which you should add your metadata
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The Excel file has two sheets:
1: Empty table into which you should add your metadata
2: A description of all the fields in the table
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3. Upload fill out metadata sheet and sequence files
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Results Summary
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Sample manager 1.Single service results 2.Download files 3.Download metadata and result data 4.Rerun of services
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Re-running individual services with changed settings
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Future developments