Qingpeng Zhang developed a bottom-up computational approach called khmer to investigate microbial diversity through k-mer counting and analysis of metagenomic sequencing data. He contributed algorithms, code and analysis methods to khmer from 2008-present. His work involved digital normalization, diversity analysis of k-mers and reads, and genome assembly and binning of symbionts. Future work will apply these methods to datasets like MetaHIT, HMP and GPGC to refine pipelines and statistical methods for informative genomic segment analysis of diversity.

1. The Story of My Research
developing a bottom-up computational approach to
investigate microbial diversity
Qingpeng Zhang
Department of Computer Science and Engineering
Michigan State University
Supervisor: Dr. Titus Brown

2. odyssey?
The Story of My Research
developing a bottom-up computational approach to
investigate microbial diversity
Qingpeng Zhang
Department of Computer Science and Engineering
Michigan State University
Supervisor: Dr. Titus Brown

3. khmer
developing a bottom-up computational approach to
development
start study/research metagenomics
digital
normalization
diversity
analysis on k-mer
level
2008
2009
2010
2011
2012
2013
2014
Osedax
diversity Symbionts
analysis on
read level(IGS)
GPGC
soil
sample
investigate microbial diversity

4. 2008: metagenomics

5. 2008: metagenomics
“Big Data!”

6. Microbial diversity
2009: microbial diversity
assembly
binning/annotation
reference
similarity-based composition-based

7. How many stuffs are there in the sample? - alpha diversity
How different are the samples? - beta diversity
Microbial diversity
2009: microbial diversity
assembly
binning/annotation
reference
similarity-based composition-based

8. Microbial diversity
2009: microbial diversity
assembly
"Nothing works, everything binning/annotation
sucks."
reference
similarity-based composition-based

9. Microbial diversity
2009: microbial diversity
assembly
NO!
binning/annotation
reference
similarity-based composition-based

10. 2009: k-mer counting

11. khmer
development
start study/research metagenomics
digital
normalization
diversity
analysis on k-mer
level
Osedax
diversity Symbionts
analysis on
read level(IGS)
GPGC
soil
sample
2008
2009
2010
2011
2012
2013
2014
developing a bottom-up computational approach to
investigate microbial diversity

12. 2010 －now: GPGC
How many stuffs are there in the sample? - alpha diversity
How does agricultural soil differ from native soil? - beta diversity

13. khmer
development
start study/research metagenomics
digital
normalization
diversity
analysis on k-mer
level
Osedax
diversity Symbionts
analysis on
read level(IGS)
GPGC
soil
sample
2008
2009
2010
2011
2012
2013
2014
developing a bottom-up computational approach to
investigate microbial diversity

14. 2010 －now: khmer

15. 2010 －now: khmer

16. 2010 －now: khmer
• My contributions:
• algorithm design/analysis, exploring the mathematics behind, the choice of optimal
parameters
• contributing codes, including unique k-mers counting, overlap k-mer counting, optimal
parameter choice, others related to my specific research project.
• benchmarking, testing, actually using it.
• exploration of applications like error trimming, filter low abundance reads, digital
normalization, etc. suggestion on features
• work on the khmer manuscript

17. 2010 －now: khmer
• My contributions:
• algorithm design/analysis, exploring the mathematics behind, the choice of optimal
parameters
• contributing codes, including unique k-mers counting, overlap k-mer counting, optimal
parameter choice, others related to my specific research project.
• benchmarking, testing, actually using it.
• exploration of applications like error trimming, filter low abundance reads, digital
normalization, etc. suggestion on features
• work on the khmer manuscript

18. khmer
development
start study/research metagenomics
digital
normalization
diversity
analysis on
k-mer level
Osedax
diversity Symbionts
analysis on
read level(IGS)
GPGC
soil
sample
2008
2009
2010
2011
2012
2013
2014
developing a bottom-up computational approach to
investigate microbial diversity

19. 2010 －2012: diversity analysis on k-mer level

20. 2010 －2012: diversity analysis on k-mer level

21. khmer
development
start study/research metagenomics
digital
normalization
diversity
analysis on k-mer
level
Osedax
diversity Symbionts
analysis on
read level(IGS)
GPGC
soil
sample
2008
2009
2010
2011
2012
2013
2014
developing a bottom-up computational approach to
investigate microbial diversity

22. 2011-2012: diginorm
median k-mer frequency to represent
the sequencing coverage of the
read
useful for diversity analysis
Digital normalization
removing redundant reads
useful for assembly

23. 2011-2012: diginorm
median k-mer frequency to represent
the sequencing coverage of the
read
useful for diversity analysis
Digital normalization
removing redundant reads
useful for assembly

24. khmer
development
start study/research metagenomics
digital
normalization
diversity
analysis on k-mer
level
Osedax
diversity Symbiont
analysis on
read level(IGS)
GPGC
soil
sample
2008
2009
2010
2011
2012
2013
2014
developing a bottom-up computational approach to
investigate microbial diversity

25. 2012-2013 symbionts
My contributions:
• diginorm/assembly/binning/
annotation
• genome completeness estimation
• 94% complete Rs1
• 66-89% complete Rs2
• some transcriptome analysis
• Other bioinformatics support

26. khmer
development
start study/research metagenomics
digital
normalization
diversity
analysis on k-mer
level
Osedax
Symbionts
diversity
analysis on
read
level(IGS)
GPGC
soil
sample
2008
2009
2010
2011
2012
2013
2014
developing a bottom-up computational approach to
investigate microbial diversity

27. 2012 －now: diversity analysis on read level

28. 2012 －now: diversity analysis on read level
IGS(informative genomic
segment) can represent
the novel information of a
genome
We can use all the data,
not only the data we
understand!

29. AFGH
FGHI
ABCE
AABC
ABCD
AAAB
ABCD FGHI ABCE AFGH
AABC
AAAB

30. AFGH
FGHI
ABCE
AABC
ABCD
AAAB
ABCD FGHI ABCE AFGH
AABC
AAAB

31. Improve the pipeline
khmer diginorm error correction

32. Sorcerer II Global Ocean Sampling Expedition

35. 2010 －now: GPGC

36. khmer
development
start study/research metagenomics
digital
normalization
diversity
analysis on k-mer
level
Osedax
diversity Symbionts
analysis on
read level(IGS)
GPGC
soil
sample
2008
2009
2010
2011
2012
2013
2014
developing a bottom-up computational approach to
investigate microbial diversity

37. 37
Future work
• Finish the IGS based diversity analysis paper
• Refine pipeline/adjust statistical method to fit IGSs
• More real data sets
• MetaHIT(Metagenomics of the Human Intestinal Tract) (working..)
• HMP (Human Microbiome Project) (working..)
• GPGC(Soil) (working..)
• Ballast water virome (working..)
• Finish a review of the methods and applications of k-mer counting in
bioinformatics (will also be part of my dissertation)
• Expand the application of IGS
• sequencing depth/effort estimation, genome size estimation
• reads binning/classification based on coverage profile across samples
• relate IGS to phylogenetic info and function
• extract IGS(reads) according different coverage profile (shared by all

38. Acknowledgement
● Dr. Titus Brown
● Lab members of GED
● Elijah Lowe
● Jiarong Guo
● Camille Scott
● Michael Crusoe
● Luiz Irber
● Dr. Sherine Awad
● Former members of GED
● Dr. Adina Howe
● Eric McDonald
● Dr. Jason Pell
● Dr. Likit Preeyanon
● RDP
● Dr. Jim Cole
● Jordan Fish