This is a brief explanation of WhAlly project.

1. Hardware acceleration of the
Burrows-Wheeler Alignment
jessica.leoni@mail.polimi.it
riccardo1.cavadini@mail.polimi.it
guidowalter.didonato@mail.polimi.it
Jessica Leoni
Riccardo Cavadini
Guido Walter Di Donato

2. 2
The Context
• The bottleneck in genomics approaches is becoming
less and less about data generation and more and
more about data management, integration, analysis,
and interpretation1.
1 - Alyass, Akram, Michelle Turcotte, and David Meyre. "From big data analysis to personalized medicine for all: challenges
and opportunities." BMC medical genomics 8.1 (2015): 33.
• Genomics for personalized
medicine is a vastly growing
and promising field.

3. 3
The Problem
1 - Alyass, Akram, Michelle Turcotte, and David Meyre. "From big data analysis to personalized medicine for all: challenges
and opportunities." BMC medical genomics 8.1 (2015): 33.
3,116,480
characters
3,088,286,401
characters

4. 3
The Problem
1 - Alyass, Akram, Michelle Turcotte, and David Meyre. "From big data analysis to personalized medicine for all: challenges
and opportunities." BMC medical genomics 8.1 (2015): 33.
3,116,480
characters
3,088,286,401
characters

5. 3
The Problem
1 - Alyass, Akram, Michelle Turcotte, and David Meyre. "From big data analysis to personalized medicine for all: challenges
and opportunities." BMC medical genomics 8.1 (2015): 33.
3,116,480
characters
3,088,286,401
characters
PROBLEMS:
STRING MATCHING TIME
SIZE OF THE DATA

6. 4
The Idea
• Whole genome indexing through the Burrows-Wheeler
Transform2, which allows:
✓ Compression of the input genome
✓ Alignment of substring, even with mismatches.
2 - Burrows M and Wheeler D, A block sorting lossless data compression algorithm, Technical Report 124, Digital
Equipment Corporation, 1994.
• Hardware implementation
exploiting FPGA architecture to
achieve better performances.

7. 5
Images from thenounproject.com
The Application
G
enom
e
Substrings
The user provides source files and simply gets results,
even without any knowledge of the underlying architecture.

8. Riccardo Cavadini
Jessica Leoni whallynecst@gmail.com
Thank you for your attention!
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