Slides from my talk given at the AWS Loft event in Stockholm, November 2018. When genomic data is staged for analysis on Amazon S3, researchers have fast access to large volumes of data without needing to download and store their own copies. In this session, you will learn how a researcher at Sweden's SciLifeLab has made reference genome data available in the cloud as an AWS Public Dataset, and how this makes it easier for researchers to do large scale genomic analysis using tools like EMR and AWS Batch.

1. Phil Ewels
NGI Applications Development Facility
phil.ewels@scilifelab.se
The Future of Genomics in the Cloud

2. ROYAL INSTITUTE
OF TECHNOLOGY

3. 8
Platforms
37
Facilities
163
Research
groups

4. Guidelines
and support
Available to all
Swedish researchers
State-of-the-art
infrastructure

5. Meetings
QC & Library
Preparation
Sequencing
Genotyping
Data analysis
& delivery

6. I N T R O T O G E N O M I C S

7. 25 μm
30-40 trillion cells
30,000,000,000,000

8. 6 μm 2 m
1 cell's worth of DNA

9. 2 m
1 cell's worth of DNA
80
billion
km
1 Human's worth of DNA
(diameter of solar system)
(×2)
Your genome
40 trillion copies
of your genome

10. Human genome:
3.2ish billion DNA base pairs
Adenine
Cytosine
Thymine
Guanine

11. Human genome:
3.2ish billion DNA base pairs
Human Genome Volume One, Wellcome Collection 2005
Photos: Wellcome Library, London

13. ACTG

14. I N T R O T O G E N O M I C S
(picture version)

28. Cost per Human Genome

29. The first Human
genome took
13 years
to sequence
In 2016 at NGI Stockholm,
we sequenced a human genome equivalent
every 4.08 minutes
Cost per Human Genome
~200TB data delivered to research groups
4k CPU cores, 64TB RAM, ~2PB disk

30. G E N O M I C S A N A LY S I S

31. Human genome:
3.2ish billion DNA base pairs
..ACTGACTCTTAGCTATGGCTCTCTAGCTAGCTACGCTACTCGACTACGACTCGCTATCGCTAGCTATATATATTTCGATCGGCGCTATC..
TCTTAGCTATGGCTC CTCGCTATCGCTAGCTA
AGCTACGCTACTCGACTA
TTTCGATCGGCGC
DNA sequencing data:
50 DNA base pairs in a "read"
Between 10 and 350 million of them, per sample

32. TCTTAGCTATGGCTC CTCGCTATCGCTAGCTA
AGCTACGCTACTCGACTA
TTTCGATCGGCGC
A "reference genome"
..ACTGACTCTTAGCTATGGCTCTCTAGCTAGCTACGCTACTCGACTACGACTCGCTATCGCTAGCTATATATATTTCGATCGGCGCTATC..

33. TCTTAGCTATGGCTC CTCGCTATCGCTAGCTAAGCTACGCTACTCGACTA TTTCGATCGGCGC
"Alignment" to the reference genome
A "reference genome"
..ACTGACTCTTAGCTATGGCTCTCTAGCTAGCTACGCTACTCGACTACGACTCGCTATCGCTAGCTATATATATTTCGATCGGCGCTATC..

34. TCTTAGCTATAGCTC CTCGCTATCTCTAGCTAAGCTACGCTACTCGACTA TTTCGATCGGCGC
..ACTGACTCTTAGCTATGGCTCTCTAGCTAGCTACGCTACTCGACTACGACTCGCTATCGCTAGCTATATATATTTCGATCGGCGCTATC..
ACGACTCGCTATCTCTA
GCTATCTCTAGCTATAT
CTCTAGCTATATATAT
CGACTCGCTATCTCTAG
CTGACTCTTAGCTATGG
TTAGCTATGGCTCTCTA
CTCTTAGCTATGGCTCT
Disease causing mutation?
Normal Cancer Relapse

35. Multiple
species
Multiple
genome
versions
Multiple
alignment
tools
Lots of files!
A "reference genome"
..ACTGACTCTTAGCTATGGCTCTCTAGCTAGCTACGCTACTCGACTACGACTCGCTATCGCTAGCTATATATATTTCGATCGGCGCTATC..

37. https://registry.opendata.aws/aws-igenomes/
https://support.illumina.com/sequencing/
sequencing_software/igenome.html
iGenomes

41. https://ewels.github.io/AWS-iGenomes/

42. A N A LY S I S P I P E L I N E S

43. Automated
Reliable
Easy for others to run
Reproducible results
Parallelisable

45. nextflow run main.nf --reads "*.fastq.gz"
Singularity

46. nextflow run fastqc.nf --reads "*.fastq.gz"

47. SGE
LSF
PBS/Torque
NQSII
HTCondor
Ignite
GA4GH TES

48. 1 1 2 3
work
results
+

51. https://nf-co.re/

54. +
+
AWS iGenomes
Traditional
HPC
and

55. ngisweden.scilifelab.se
opensource.scilifelab.se
NGI Stockholm
Maxime Garcia
Johannes Alneberg
Max Käller
Remi-Andre Olsen
Chuan Wang
Denis Moreno
Rickard Hammarén
Senthil Panneerselvam
QBiC Tübingen
Sven Fillinger
Alexander Peltzer
GIS Singapore
Andreas Wilm
Chih Chuan
CRG Barcelona
Paolo Di Tommaso
Phil Ewels
phil.ewels@scilifelab.se
ewels
tallphil
nf-co.re
ngisweden
AWS Cloud Credits for Research
sarek.scilifelab.se
Icons: flaticon.com

56. ngisweden.scilifelab.se
opensource.scilifelab.se
Phil Ewels
phil.ewels@scilifelab.se
ewels
tallphil
sarek.scilifelab.se
nf-co.re
We're hiring!
Systems / devops
No biology background
required
ngisweden
Icons: flaticon.com