Talk at Oregon State University, Mar 10, 2015.

1. C . T I T U S B R O W N
C T B R O W N @ U C D A V I S . E D U
A S S O C I A T E P R O F E S S O R
P O P U L A T I O N H E A L T H A N D R E P R O D U C T I O N
S C H O O L O F V E T E R I N A R Y M E D I C I N E
U N I V E R S I T Y O F C A L I F O R N I A , D A V I S
Concepts and tools for exploring
very large sequencing data sets.

2. Some background & motivation:
 We primarily build tools to look at large sequencing
data sets.
 Our interest is in enabling scientists to move quickly
to hypotheses from data.

3. My goals
 Enable hypothesis-driven biology through better
hypothesis generation & refinement.
 Devalue “interest level” of sequence analysis and put
myself out of a job.
 Be a good mutualist!

4. Narrative arc
1. Shotgun metagenomics: can we reconstruct
community genomes?
2. Underlying technology-enabled approach – tools
and platforms are good.
3. My larger plan for world domination through
technology and training – a kinder, gentler world
(?).

5. Shotgun metagenomics
 Collect samples;
 Extract DNA;
 Feed into sequencer;
 Computationally analyze.
Wikipedia: Environmental shotgun
sequencing.png

6. Shotgun sequencing & assembly
http://eofdreams.com/library.html;
http://www.theshreddingservices.com/2011/11/paper-shredding-services-small-business/;
http://schoolworkhelper.net/charles-dickens%E2%80%99-tale-of-two-cities-summary-analysis/

7. To assemble, or not to assemble?
Goals: reconstruct phylogenetic content and predict
functional potential of ensemble.
 Should we analyze short reads directly?
OR
 Do we assemble short reads into longer contigs first,
and then analyze the contigs?

8. Howe et al., 2014
Assemblies yield much
more significant
similarity matches.
Assembly: good for annotation!

9. But! Isn’t assembly problematic?
 Chimeric misassemblies?
 Uneven coverage?
 Strain variation?
 Computationally challenging?

10. I. Benchmarking metagenome assembly
 Most assembly papers analyze novel data sets and
then have to argue that their result is ok (guilty!)
 Very few assembly benchmarks have been done.
 Even fewer (trustworthy) computational
time/memory comparisons have been done.
 And even fewer “assembly recipes” have been
written down clearly.

11. Shakya et al., 2013; pmid 23387867

12. A mock community!
 ~60 genomes, all sequenced;
 Lab mixed with 10:1 ratio of most abundant to least
abundant;
 2x101 reads, 107 mn reads total (Illumina);
 10.5 Gbp of sequence in toto.
 The paper also compared16s primer sets & 454
shotgun metagenome data => reconstruction.
Shakya et al., 2013; pmid 23387867

13. Paper conclusions
 “Metagenomic sequencing outperformed most SSU
rRNA gene primer sets used in this study.”
 “The Illumina short reads provided a very good estimates
of taxonomic distribution above the species level, with
only a two- to threefold overestimation of the actual
number of genera and orders.”
 “For the 454 data … the use of the default parameters
severely overestimated higher level diversity (~ 20- fold
for bacterial genera and identified > 100 spurious
eukaryotes).”
Shakya et al., 2013; pmid 23387867

14. How about assembly??
 Shakya et al. did not do assembly; no standard for
analysis at the time, not experts.
 But we work on assembly!
 And we’ve been working on a tutorial/process for
doing it!

15. Adapter trim &
quality filter
Diginorm to C=10
Trim high-
coverage reads at
low-abundance
k-mers
Diginorm to C=5
Partition
graph
Split into "groups"
Reinflate groups
(optional
Assemble!!!
Map reads to
assembly
Too big to
assemble?
Small enough to assemble?
Annotate contigs
with abundances
MG-RAST, etc.
The Kalamazoo Metagenomics Protocol
Derived from approach used in Howe et al., 2014

16. Computational protocol for assembly

17. Adapter trim &
quality filter
Diginorm to C=10
Trim high-
coverage reads at
low-abundance
k-mers
Diginorm to C=5
Partition
graph
Split into "groups"
Reinflate groups
(optional
Assemble!!!
Map reads to
assembly
Too big to
assemble?
Small enough to assemble?
Annotate contigs
with abundances
MG-RAST, etc.
Kalamazoo Metagenomics Protocol => benchmarking!
Assemble with Velvet, IDBA, SPAdes

18. Benchmarking process
 Apply various filtering treatments to the data (x3)
 Basic quality trimming and filtering
 + digital normalization
 + partitioning
 Apply different assemblers to the data for each
treatment (x3)
 IDBA
 SPAdes
 Velvet
 Measure compute time/memory req’d.
 Compare assembly results to “known” answer with
Quast.

19. Recovery, by assembler
Velvet IDBA Spades
Quality Quality Quality
Total length (>= 0 bp) 1.6E+08 2.0E+08 2.0E+08
Total length (>= 1000 bp) 1.6E+08 1.9E+08 1.9E+08
Largest contig 561,449 979,948 1,387,918
# misassembled contigs 631 1032 752
Genome fraction (%) 72.949 90.969 90.424
Duplication ratio 1.004 1.007 1.004
Conclusion: SPAdes and IDBA achieve similar results.
Dr. Sherine Awad

20. Treatments do not alter results very much.
IDBA
Default Diginorm Partition
Total length (>= 0 bp) 2.0E+08 2.0E+08 2.0E+08
Total length (>= 1000 bp) 1.9E+08 2.0E+08 1.9E+08
Largest contig 979,948 1,469,321 551,171
# misassembled contigs 1032 916 828
Unaligned length 10,709,716 10,637,811 10,644,357
Genome fraction (%) 90.969 91.003 90.082
Duplication ratio 1.007 1.008 1.007
Dr. Sherine Awad

21. Treatments do save compute time.
Velvet idba Spades
Time
(h:m:s)
RAM
(gb)
Time
(h:m:s)
RAM
(gb)
Time
(h:m:s)
RAM
(gb)
Quality 60:42:52 1,594 33:53:46 129 67:02:16 400
Diginorm 6:48:46 827 6:34:24 104 15:53:10 127
Partition 4:30:36 1,156 8:30:29 93 7:54:26 129
(Run on Michigan State HPC)
Dr. Sherine Awad

22. Need to understand:
 What is not being assembled and why?
 Low coverage?
 Strain variation?
 Something else?
 Effects of strain variation: no assembly.
 Additional contigs being assembled –
contamination? Spurious assembly?

23. Assembly conclusions
 90% recovery is not bad; relatively few
misassemblies, too.
 This was not a highly polymorphic community BUT
it did have several closely related strains; more
generally, we see that strains do generate chimeras,
but not between different species.
 …challenging to execute even with a
tutorial/protocol.

24. We need much deeper sampling!
Sharon et al., 2015 (Genome Res)
Overlap between synthetic long reads and short reads.

25. Benchmarking & protocols
 Our work is completely reproducible and open.
 You can re-run our benchmarks yourself if you want!
 We will be adding new assemblers in as time
permits.
 Protocol is open, versioned, citable… but also still a
work in progress :)

26. II: Shotgun sequencing and coverage
“Coverage” is simply the average number of reads that overlap
each true base in genome.
Here, the coverage is ~10 – just draw a line straight down from the
top through all of the reads.

27. Assembly depends on high coverage
HMP mock community

28. Main questions --
I. How do we know if we’ve sequenced enough?
II. Can we predict how much more we need to
sequence to see <insert some feature here>?
Note: necessary sequencing depth cannot
accurately be predicted solely from
SSU/amplicon data

29. Method 1: looking for WGS saturation
We can track how many sequences we
keep of the sequences we’ve seen, to
detect saturation.

30. Data from Shakya et al., 2013 (pmid: 23387867
We can detect saturation of
shotgun sequencing

31. Data from Shakya et al., 2013 (pmid: 23387867
We can detect saturation of
shotgun sequencing
C=10, for assembly

32. Sample A Sample B
Coverage = 8
Reads are noisy observations of genomic regions.
Qingpeng Zhang

33. v Sample
1
Sample
2
Sample
3
Sample
4
Sample
5
Sample
6
SpeciesA 3 3 4 4 0 0
SpeciesB 1 3 0 2 2 2
SpeciesC 1 2 2 2 3 3
SpeciesD 2 1 2 1 1 1
SpeciesE 4 1 3 0 2 5
SpeciesF 5 1 2 2 2 5
SpeciesG 2 2 1 2 1 3
SpeciesG 4 1 3 0 2 5
5 1 2 2 2 5
2 2 1 2 1 3
Alpha diversity:
“How many different species in a soil sample?”
Beta diversity:
“How different are the soil samples”
Can we use read coverage analysis for alpha and beta diversity estimation?
Qingpeng Zhang

34. Can estimate total size of metagenome using
(e.g.) Chao1
Qingpeng Zhang

35. Soil sample clustering on WGS – Great Prairie data
Qingpeng Zhang

36. Can we predict how much sequencing we need?
 Tells us when we have enough sequence.
 Can’t be predictive… if you haven’t sampled
something, you can’t say anything about it.
Can we correlate deep amplicon sequencing with
shallower WGS?

37. Correlating 16s and shotgun WGS
How
much
of 16s
do you
see…
with how much shotgun sequencing?

38. Data from Shakya et al., 2013 (pmid: 23387867)
WGS saturation ~matches 16s saturation
< rRNA copy
number >

39. Method is robust to organisms unsampled by
amplicon sequencing.
Insensitive to
amplicon primer
bias.
Robust to genome
size differences,
eukaryotes, phage.
Data from Shakya et al., 2013 (pmid: 23387867

40. Can examine specific OTUs
Data from Shakya et al., 2013 (pmid: 23387867

41. OTU abundance is ~correct.
Data from Shakya et al., 2013 (pmid: 23387867

42. Running on real communities --

43. Running on real communities --

44. Concluding thoughts on metagenomes -
 The main obstacle to recovering genomic details of
communities is shallow sampling.
 Considerably deeper sampling is needed – 1000x
(petabasepair sampling)
 This will inevitably happen!
 …I would like to make sure the compute technology
is there, when it does.

45. More general: computation needs to scale!
Navin et al., 2011

46. Cancer investigation ~ metagenome investigation
Some basic math:
 1000 single cells from a tumor…
 …sequenced to 40x haploid coverage with Illumina…
 …yields 120 Gbp each cell…
 …or 120 Tbp of data.
 HiSeq X10 can do the sequencing in ~3 weeks.
 The variant calling will require 2,000 CPU weeks…
 …so, given ~2,000 computers, can do this all in one month.
 …but this will soon be done ~100s-1000s of times a month.

47. Similar math applies:
 Pathogen detection in blood;
 Environmental sequencing;
 Sequencing rare DNA from circulating blood.
 Two issues:
Volume of data & compute
infrastructure;
Latency in turnaround.

48. Streaming algorithms are good for biggish data…
1-pass
Data
Answer

49. Raw data
(~10-100 GB) Analysis
"Information"
~1 GB
"Information"
"Information"
"Information"
"Information"
Database &
integration
Compression
(~2 GB)
Lossy compression can substantially
reduce data size while retaining
information needed for later (re)analysis.
…as is lossy compression.

50. Moving all sequence analysis generically to
semi-streaming:
~1.2 pass, sublinear memory
Paper at: https://github.com/ged-lab/2014-streaming

51. Moving some sequence analysis to streaming.
~1.2 pass, sublinear memory
Paper at: https://github.com/ged-lab/2014-streaming
First pass: digital normalization - reduced set of k-mers.
Second pass: spectral analysis of data with reduced k-mer set.
First pass: collection of low-abundance reads + analysis of saturated reads.
Second pass: analysis of collected low-abundance reads.
First pass: collection of low-abundance reads + analysis of saturated reads.
(a)
(b)
(c)
two-pass;
reduced memory
few-pass;
reduced memory
online; streaming.

52. Five super-awesome technologies…
1. Low-memory k-mer counting
(Zhang et al., PLoS One, 2014)
2. Compressible assembly graphs
(Pell et al., PNAS, 2012)
3. Streaming lossy compression of sequence data
(Brown et al., arXiv, 2012)
4. A semi-streaming framework for sequence analysis
5. Graph-alignment approaches for fun and profit.

53. …implemented in one super- awesome software
package.
github.com/ged-lab/khmer/
BSD licensed
Openly developed using good practice.
> 30 external contributors.
Thousands of downloads/month.
100+ citations in 4 years.
We think > 5000 people are using it; have heard
from 100s. Bundled with software that ~100k people
are using.

54. How can we move from data to hypotheses more
quickly?
Build robust, flexible computational frameworks for
data exploration.
Develop theory, algorithms, software together, and
train people in its use.
(And stop building black-box analysis software that
purports to “give you the answer”.)

55. What’s next?
In transition! MSU to UC Davis.
 So, uh, I joined a Vet Med school -
“Companion animals have genomes too!”
 Expanding my work more to genomic…
 Co-incident to moving to Davis, I also became a
Moore Foundation Data Driven Discovery
Investigator.

56. Tackling data availability…
In 5-10 years, we will have nigh-infinite data.
(Genomic, transcriptomic, proteomic, metabolomic,
…?)
We currently have no good way of querying,
exploring, investigating, or mining these data sets,
especially across multiple locations..
Moreover, most data is unavailable until after
publication…
…which, in practice, means it will be lost.

57. …and data integration.
Once you have all the data, what do you do?
"Business as usual simply cannot work."
Looking at millions to billions of genomes.
(David Haussler, 2014)

58. Funded: distributed graph database server
Compute server
(Galaxy?
Arvados?)
Web interface + API
Data/
Info
Raw data sets
Public
servers
"Walled
garden"
server
Private
server
Graph query layer
Upload/submit
(NCBI, KBase)
Import
(MG-RAST,
SRA, EBI)
ivory.idyll.org/blog/2014-moore-ddd-award.html

59. The larger research vision:
100% buzzword compliantTM
Enable and incentivize sharing by providing
immediate utility; frictionless sharing.
Permissionless innovation for e.g. new data
mining approaches.
Plan for poverty with federated infrastructure
built on open & cloud.
Solve people’s current problems, while
remaining agile for the future.
ivory.idyll.org/blog/2014-moore-ddd-award.html

60. Education and training
Biology is underprepared for data-intensive
investigation.
We must teach and train the next generations.
~10-20 workshops / year, novice -> masterclass; open
materials.
Deeply self-interested:
What problems does everyone have, now?
(Assembly)
What problems do leading-edge researchers have?
(Data integration)
dib-training.rtfd.org/

61. Thanks!
Please contact me at ctbrown@ucdavis.edu!