NVIDIA Parabricks v4.3.1 Enhances Genomic Analysis with Deep Learning

NVIDIA
has
announced
the
release
of
Parabricks
v4.3.1,
a
significant
upgrade
to
its
genomic
analysis
software,
according
to
the

NVIDIA
Technical
Blog.
This
latest
version
introduces
new
functionalities
for
variant
calling
in
somatic
data,
enhancing
the
computational
efficiency
and
accuracy
of
genomic
studies.

Variant
Calling
for
Genomic
Analysis

Variant
calling
is
a
critical
process
in
high-throughput
sequencing,
enabling
scientists
to
identify
variants
across
whole
genomes,
exomes,
and
gene
panels.
This
process
is
essential
for
understanding
diseases
and
developing
potential
treatments.
However,
it
is
computationally
intensive,
especially
for
whole-genome
sequencing,
requiring
significant
resources
for
sequence
alignment
and
variant
detection.

DeepVariant
for
Germline
Data

DeepVariant,
a
deep-learning–based
variant
caller
developed
by
Google,
is
one
of
the
most
popular
tools
for
germline
variant
detection.
It
reduces
false
positives
and
detects
variants
that
traditional
methods
often
miss.
In
the
latest
Parabricks
release,
DeepVariant
has
been
upgraded
to
version
1.6.1,
offering
improved
performance
in
GPU-accelerated
germline
variant
calling.

DeepSomatic
for
Somatic
Data

DeepSomatic,
the
somatic
counterpart
to
DeepVariant,
has
been
integrated
into
Parabricks
v4.3.1.
Somatic
variants,
which
occur
after
conception
and
affect
non-reproductive
cells,
are
not
hereditary
and
happen
randomly.
DeepSomatic
provides
high-accuracy
variant
calling
for
somatic
data
and
is
now
supported
for
short-read
sequencing
in
the
Parabricks
platform.

“High-accuracy
deep-learning
tools
like
DeepSomatic
are
critical
to
advancing
genomics
research
and
deepening
our
understanding
of
somatic
mutations,”
said
Francisco
Garcia,
Ph.D.,
senior
vice
president
of
Informatics
at
Element
Biosciences.
“Combined
with
Element’s
high-quality
Q50-enabled
UltraQ
sequencing,
they
provide
a
powerful
solution
for
analyzing
high-depth
cancer
genomes.”

Minimap2
v2.26
Upgrade
in
NVIDIA
Parabricks

Minimap2,
a
popular
tool
for
aligning
long-read
sequences,
has
also
been
upgraded
to
version
2.26
in
Parabricks
v4.3.1.
This
upgrade
includes
improved
splice
alignment
for
RNA
sequencing
data
and
better
integration
with
long-read
sequencing
platforms
like
PacBio.

“This
latest
release
of
Parabricks
includes
the
same
version
of
Minimap2
used
by
the
pbmm2
read
aligner
from
PacBio,”
explained
Aaron
Wegner,
senior
director
of
product
management
at
PacBio.
“I
am
excited
to
see
partners
like
NVIDIA
continuing
to
make
it
easier
and
faster
to
analyze
HiFi
long
reads
from
our
game-changing
Revio
system.”

Parabricks
Benchmarks

With
each
release,
NVIDIA
aims
to
improve
benchmark
performance
across
instruments,
tools,
and
GPUs.
Table
1
outlines
the
latest
benchmarks
from
the
previous
Parabricks
v4.3
release,
showcasing
the
performance
on
popular
NVIDIA
GPUs
like
the
H100
for
speed
and
the
L4
for
cost
efficiency.

30x
whole
genome
sequenced
for
FQ2BAM,
BWA-Meth,
DeepVariant,
and
Haplotype
Caller
with
Illumina
data. 
50x
tumor-normal
whole
genome
sequenced
for
Mutect2
with
Illumina
data.

Get
Started

With
the
latest
4.3.1
release,
scientists
and
researchers
conducting
cancer
sequencing
can
now
access
DeepSomatic
for
short-read
sequencing.
Parabricks
4.3.1
accelerates
the
deep-learning–based
approach
from
Google
by
powering
an
easy-to-use,
accelerated
version
for
somatic
variant
calling.

Image
source:
Shutterstock

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