Next-Gen Sequencing Analysis by GigaGalaxy

Tin-Lap, LEESchool of Biomedical Sciences

CUHK-BGI Innovation Institute of Trans-omics,The Chinese University of Hong Kong

CUHK-BGI Innovation Institute of Trans-

Omics (CBIIT)

• Jointly established between The Chinese University of Hong Kong (CUHK) and BGI in July 2011.

• “We aim to provide a platform conductive to training of multi-disciplinary talents conversant with the knowledge and application of genomics, proteomics, genetics, computation biology and bioinformatics, by capitalizing on both institutions’ expertise and strengths in genomic science.”

Galaxy

http://galaxyproject.org/

www.gigasciencejournal.com

Journal, data-platform and database for large-scale data

Editor-in-Chief: Laurie GoodmanExecutive Editor: Scott Edmunds

Commissioning Editor: Nicole NogoyLead Curator: Chris Hunter

Data Platform: Peter Li

in conjunction with

GigaDB

Giga-Galaxy Collaboration between GigaScience and CBIIT

A publicly accessible Galaxy Servers

Share some of the workload of the main Galaxy server

Host data and workflows published in GigaScience, particularly involving NGS data analysis

SOAP package: advantages from GigaGalaxy

Application Instance: SOAPdenovo2 tool

http://www.cuhk.edu.hk/cbiit/galaxy.html

Galaxy/CUHK-BGI

Import data from GigaDB to

GigaGalaxy

GigaSolution: deconstructing the paper

www.gigadb.orgwww.gigasciencejournal.com

galaxy.cbiit.cuhk.edu.hk

Combines and integrates:

Open-access journal

Data Publishing Platform

Data Analysis Platform

doi:10.1186/2047-217X-1-18doi:10.5524/100038

AnalysisData Methods

doi:10.5524/100044+ =

Wang J et al., (2012): Updated genome assembly of YH: the first diploid genome sequence of a Han Chinese individual (version 2, 07/2012). GigaScience Database. http://dx.doi.org/10.5524/100038

Luo R et al., (2012): Software and supporting material for “SOAPdenovo2: An empirically improved memory-efficient short read de novo assembly”. GigaScience Database. http://dx.doi.org/10.5524/100044

Data

Methods

Luo R et al., (2012): SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler GigaScience, 1:18 (28th December 2012) http://dx.doi.org/10.1186/2047-217X-1-18

Analysis

Example

CBIIT GigaGalaxy Structure

ToolDevelopment PublishingBiomedical and bioinformatics research

What is SOAP?• SOAP - a tool package that provides full solution to NGS data analysis by BGI.

http://soap.genomics.org.cn/

SOAPdenovo2 tools An assembly tool for short reads generated from

NGS technology

Four modules Pregraph: construct bruijn graph Contig: identification from overlapping sequence reads Map: reads onto contigs Scaff: generate final assembly results

Generate 1. Contig and 2. Scaffold files

SOAPdenovo2 in GigaGalaxy

Integrate BGI SOAP tools into Giga-

Galaxy

Assembly Supporting Tools

• SOAPfilter: removed reads with artifacts

• Kmerfreq HA: a kmer frequency counter

• Corrector HA: corrects sequencing errors in short reads

• Gapcloser: close gaps in scaffolds

Put them together

Sequencing Data SOAPfilter kmerFreq HA

Corrector HASOAPdenovo2GAGE evaluation

Soapdenovo2 Workflow

S. Aureus Dataset

GAGE

Visualization Tool: CONTIGuator2

CONTIGuator2 output

VisualizationNC_010079.pdf

gi_161510924_ref_NC_010063.1_.pdf

Help Center: Shared Data• Several Datasets are available from the shared

data menu for test-running the tools. • Data Libraries• Published Workflows• Published Pages

What is in the shared data menu?

SOAPdenovo2 tutorial

How is GigaScience supporting

data reproducibility?

Data sets

Analyses

Linked to

Linked to

DOI

DOI

Open-Paper

Open-Review

DOI:10.1186/2047-217X-1-18

~10000 accesses

Open-Code

8 reviewers tested data in ftp server & named reports published

DOI:10.5524/100044

Open-PipelinesOpen-Workflows

DOI:10.5524/100038

Open-Data

78GB CC0 data

Code in sourceforge under GPLv3: http://soapdenovo2.sourceforge.net/~5000 downloads

Enabled code to being picked apart by bloggers in wiki http://homolog.us/wiki/index.php?title=SOAPdenovo2

SOAPdenovo2 workflows implemented in

galaxy.cbiit.cuhk.edu.hk

Implemented entire workflow in GigaGalaxy server, inc.:

• 3 pre-processing steps

• 4 SOAPdenovo modules

• 1 post processing steps

• Evaluation and visualization tools

Will be available for >25K Galaxy users in Galaxy Toolshed

Acknowledgements• CUHK

• Huayuan Gao

• BGI-HK and GigaScience• Peter Li• Scott Edmunds

• Galaxy team members