Molecular
Diagnos/cs
• Development
of
new
diagnos2c
assays
and
epidemiological
surveillance
of
viral
pathogens
of
livestock
and
crops
in
East
and
Central
Africa
using
LAMP
assays
• East
Coast
fever
(ECF)
recombinant
vaccine
development
• The
plant
virome
ecology
in
African
farming
systems
Mobilizing biosciences for Africa’s development
BecA-­‐ILRI
Hub
Genomics
and
Bioinforma/cs
Pla=orms
This
document
is
licensed
for
use
under
a
Crea/ve
Commons
ACribu/on-­‐Noncommercial-­‐Share
Alike
3.0
Unported
License
May
2013
Mark
Wamalwa,
Francesca
Stomeo,
Joyce
Njuguna,
Appolinaire
Djikeng.
BecA-­‐ILRI
Hub,
Nairobi,
PO
Box
30709,
00100,
Kenya
(m.wamalwa@cgiar.org)
Highlights
from
projects
using
the
BecA-­‐ILRI
Genomics
and
Bioinforma/cs
Pla=orms
The
BecA-­‐ILRI
Hub
genomics
plaIorm
is
equipped
with
both
capillary
(ABI
3130xl,
ABI
3730xl
and
ABI
3500xl)
and
second-­‐genera2on
sequencing
(the
Roche
454
GSFLX™
Titanium
pyrosequencer
and
Illumina
MiSeq)
plaIorms
integrated
with
high
performance
compu2ng
systems.
The
Bioinforma2cs
plaIorm
leverages
on
the
current
Genomics
plaIorm
to
provide
advanced
computa2onal
services,
access
to
high
performance
compu2ng,
data
storage,
bioinforma2cs
support
and
consultancy
services
to
African
scien2sts
and
external
users.
Bioinforma2cs
offers
tremendous
opportuni2es
and
has
great
poten2al
to
underpin
biotechnological
solu2ons
to
agricultural
development
constraints.
In
a
nutshell,
bioinforma2cs
is
the
key
to
understanding
the
molecule
of
life,
DNA.
Using
these
plaIorms,
the
Hub
has
embarked
on
research
ac2vi2es
including
various
genome
(par2al
and
complete)
sequencing
projects
(cassava
re-­‐sequencing,
viral
genomics
and
metagenomics).
Metagenomics
projects
have
been
par2cularly
informa2ve,
as
they
have
provided
the
tools
to
quickly
scan
the
bacterial
and
viral
communi2es
(pathogenic
and
non-­‐pathogenic)
in
specific
ecosystems
with
the
poten2al
of
applica2ons
to
various
food
value
chains.
Hence
experimental
data
output
has
considerably
grown
in
size
and
complexity.
These
robust
plaIorms
will
significantly
increase
our
ability
to
address
major
issues
related
to
pathogens
discovery,
crops
improvement
and
food
security
and
will
con2nue
to
support
capacity
building
and
services
demands
in
the
BecA
Hub
region
and
beyond.
Capacity
Building
• Training
workshops:
a) Introduc2on
to
Molecular
Biology
and
Bioinforma2cs
Workshop
b) Advanced
Genomics
and
Bioinforma2cs
Workshop
• MSc
and
PhD
student
projects
hub.africabiosciences.org
Food
security:
Crop
and
livestock
improvement
• Bacterial
disease
resistance
in
banana
and
enset
• Late
blight
resistance
in
potato
• Weevil
resistance
in
sweet
potato
• Mosaic
virus
resistance
in
cassava.
• Maize-­‐sorghum
hybrid/molecular
marker
• Climate-­‐smart
Brachiaria
grasses
for
improving
livestock
produc2on
Key
partners
include
IITA,
CIP,
MARI
(Tanzania),
EIAR
(Ethiopia)
ILRI
Kenya
HPC
Cluster
(88
Nodes)
1.
2.
3.
4.
Quality
Control
Assembly
(De
novo/Reference)
Feature
predic2on
Data
Visualiza2on
Bioinforma/cs
Core
Ac/vi/es
Sta/s/cal
Support
• Experimental
design
Primary
Data
Analysis
• NGS
QC,
spa2al
defect
removal
• 454
GA
Pipleline
Secondary/Downstream
analysis
• Differen2al
Expression
• Structural
varia2on,
geonomic
rearrangements
• SNP
and
CN
analysis
• microRNA
profiling
• GO
enrichment
Training/Capacity
Building
• Mo2f
Finding
• Func2onal/Network
Analysis
Data
Management
• NGS
data
storage
and
manipula2on
• Data
warehouse
facili2es:
databases
Soaware
development
• Bioconductor
packages:
NGS
annota2on
packages
• Automated
NGS
analysis
packages
Bioinforma/cs
tools
• Ensembl,
Galaxy,
Cytoscape