Beyond the Command-Line Interface:

Transcriptome Analysis based on Next-Generation-Sequencing Data

Beyond the Command-Line Interface:

Transcriptome Analysis based on Next-Generation-Sequencing Data

Transcriptome Analysis

Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook

Assembly / Annotation

• cheap to produce

• fast way of producing data

• allows comparative analysis

Assembly

Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook

Assembly / Annotation

Assembly

read 1

read III

read 1V read 1I

Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook

Assembly / Annotation

Assembly

read 1 read III

read 1Vread 1I

Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook

Assembly / Annotation

Assembly

Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook

Assembly / Annotation

Assembly

Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook

Assembly / Annotation

Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook

Assembly / Annotation

Annotation

Image: http://commons.wikimedia.org/wiki/User:Rama, CC-BY-SA 2.0

Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook

Assembly / Annotation

Annotation

Image: http://commons.wikimedia.org/wiki/User:Rama, CC-BY-SA 2.0

Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook

Assembly / Annotation

Annotation

Image: http://commons.wikimedia.org/wiki/User:Rama, CC-BY-SA 2.0

Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook

Tools / Interfaces / Drawbacks

How is it done?What tools do exist?

Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook

Tools / Interfaces / Drawbacks

How is it done?

What tools do exist?

Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook

Tools / Interfaces / Drawbacks

How is it done?What tools do exist?Assembly

SNP-Detection

Homology-Detection

ORF-Prediciton

CAP3 QualitySNP BLAST ESTScan

MIRA AutoSNP FASTX/FASTY ORFPredictor

PolyBayes HMMER

MIRA PatternHunter

Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook

Tools / Interfaces / Drawbacks

Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook

Tools / Interfaces / Drawbacks

Toolword count

of the manual

BLAST2GO 618

BLAST 3469

HMMER 32213

MIRA 71654

Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook

Tools / Interfaces / Drawbacks

Chin et al, 1998

Drawbacks

• spoilt for choice by the amount of tools

• time-consuming to find right tools

• lots of parameters to learn

• the command-line interface is unintuitive

Beyond the CLIGetting around the Drawbacks

Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook

Solutions / Pipeline / GUI / Distributed Ruby

Chin et al, 1998

• minimize choice of tools

• minimize the parameters for each tool

• add a graphical user interface

PipelineTranscriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook

Solutions / Pipeline / GUI / Distributed Ruby

PipelineTranscriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook

Solutions / Pipeline / GUI / Distributed Ruby

Task Tool

File-ConversionPerl- & Python-

Scripts

Assembly MIRA

SNP-Detection MIRA

Homology-Detection

BLAST

ORF-Prediction ORFPredictor

Pfam-Annotationpfam_scan /

HMMER

GO-Annotation BLAST2GO

PipelineTranscriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook

Solutions / Pipeline / GUI / Distributed Ruby

Task Tool

File-ConversionPerl- & Python-

Scripts

Assembly MIRA

SNP-Detection MIRA

Homology-Detection

BLAST

ORF-Prediction ORFPredictor

Pfam-Annotationpfam_scan /

HMMER

GO-Annotation BLAST2GO

PipelineTranscriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook

Solutions / Pipeline / GUI / Distributed Ruby

Task Tool

File-ConversionPerl- & Python-

Scripts

Assembly MIRA

SNP-Detection MIRA

Homology-Detection

BLAST

ORF-Prediction ORFPredictor

Pfam-Annotationpfam_scan /

HMMER

GO-Annotation BLAST2GO

PipelineTranscriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook

Solutions / Pipeline / GUI / Distributed Ruby

Task Tool

File-ConversionPerl- & Python-

Scripts

Assembly MIRA

SNP-Detection MIRA

Homology-Detection

BLAST

ORF-Prediction ORFPredictor

Pfam-Annotationpfam_scan /

HMMER

GO-Annotation BLAST2GO

GUI

Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook

Solutions / Pipeline / GUI / Distributed Ruby

GUI

Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook

Solutions / Pipeline / GUI / Distributed Ruby

GUI

Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook

Solutions / Pipeline / GUI / Distributed Ruby

GUI

Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook

Solutions / Pipeline / GUI / Distributed Ruby

GUI

Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook

Solutions / Pipeline / GUI / Distributed Ruby

GUI

Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook

Solutions / Pipeline / GUI / Distributed Ruby

GUI

Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook

Solutions / Pipeline / GUI / Distributed Ruby

GUI

Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook

Solutions / Pipeline / GUI / Distributed Ruby

GUI

Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook

Solutions / Pipeline / GUI / Distributed Ruby

GUI

Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook

Solutions / Pipeline / GUI / Distributed Ruby

Distributed Ruby

Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook

Solutions / Pipeline / GUI / Distributed Ruby

Distributed Ruby

Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook

Solutions / Pipeline / GUI / Distributed Ruby

Results

Zostera marina

Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook

Zostera marina / Results

Image: Colin Faulkingham, CC-BY-SA 2.5

Results

Zostera marina

Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook

Zostera marina / Results

Image: Colin Faulkingham, CC-BY-SA 2.5

866838 454-reads

Results

Zostera marina

Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook

Zostera marina / Results

Image: Colin Faulkingham, CC-BY-SA 2.5

866838 454-reads

35364 contigs

Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook

Zostera marina / Results

Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook

Zostera marina / Results

Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook

Zostera marina / Results

Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook

Zostera marina / Results

Shortcomings

• only basic analysis due to lack of parameters of single tools

• no graphical representation of results

Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook

Shortcomings & Solutions / Summary

Shortcomings• only basic analysis due to lack of

parameters of single tools

• no graphical representation of results

Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook

Shortcomings & Solutions / Summary

Solutions• add optional “expert” parameters

• implement graphical representations

Summary

• Transcriptome Analysis needs software tools

• Many different tools for each task exist

• Most of them are CLI-driven

• People don‘t like the CLI

Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook

Shortcomings & Solutions / Summary

Summary

• Built a pipeline that provides usual tools and a GUI

• The pipeline works for standard tasks of Transcriptome Analysis

• In an upcoming version more tool-parameters & graphical results shall be added

Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook

Shortcomings & Solutions / Summary

it´s your turn: feel free to ask questions

image: Joe Rosenthal & Shigeru Miyamoto (fair use)

it´s your turn: feel free to ask questions

image: Joe Rosenthal & Shigeru Miyamoto (fair use)