Tin-Lap Lee's presentation at Bio-IT World Asia on "Next-Gen Sequencing Analysis by GigaGalaxy", 30th May 2013

1. Next-Gen Sequencing Analysis
by GigaGalaxy
Tin-Lap, LEE
School of Biomedical Sciences
CUHK-BGI Innovation Institute of Trans-omics,
The Chinese University of Hong Kong

2. 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.”

3. Galaxy
http://galaxyproject.org/

4. www.gigasciencejournal.com
Journal, data-platform and
database for large-scale data
Editor-in-Chief: Laurie Goodman
Executive Editor: Scott Edmunds
Commissioning Editor: Nicole Nogoy
Lead Curator: Chris Hunter
Data Platform: Peter Li
in conjunction with

5. GigaDB

6. 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

7. http://www.cuhk.edu.hk/cbiit/galaxy.html
Galaxy/CUHK-BGI

8. Import data from GigaDB to GigaGalaxy

9. GigaSolution: deconstructing the paper
www.gigadb.org
www.gigasciencejournal.com
galaxy.cbiit.cuhk.edu.hk
Combines and integrates:
Open-access journal
Data Publishing Platform
Data Analysis Platform

10. 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

12. CBIIT GigaGalaxy Structure
Tool
Development PublishingBiomedical and bioinformatics research

13. What is SOAP?
• SOAP - a tool package that provides full solution to NGS data analysis by BGI.
http://soap.genomics.org.cn/

14. 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

15. SOAPdenovo2 in GigaGalaxy

16. Integrate BGI SOAP tools into Giga-Galaxy

17. 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

18. Put them together
Sequencing
Data
SOAPfilter kmerFreq HA
Corrector HASOAPdenovo2GAGE evaluation

19. Soapdenovo2 Workflow

20. S. Aureus Dataset

21. GAGE

22. Visualization Tool: CONTIGuator2

23. CONTIGuator2 output

24. Visualization
NC_010079.pdf
gi_161510924_ref_NC_010063.1_.pdf

25. Help Center: Shared Data
• Several Datasets are available from the shared data menu
for test-running the tools.
• Data Libraries
• Published Workflows
• Published Pages

26. What is in the shared data menu?

27. SOAPdenovo2 tutorial

29. How is GigaScience supporting data
reproducibility?
Data sets
Analyses
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-Pipelines
Open-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

30. 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

31. Acknowledgements
• CUHK
• Huayuan Gao
• BGI-HK and GigaScience
• Peter Li
• Scott Edmunds
• Galaxy team members