Uncalled4 improves nanopore DNA and RNA modification detection via fast and accurate signal alignment
Nature Methods,
Journal Year:
2025,
Volume and Issue:
unknown
Published: March 28, 2025
Nanopore
signal
analysis
enables
detection
of
nucleotide
modifications
from
native
DNA
and
RNA
sequencing,
providing
both
accurate
genetic
or
transcriptomic
epigenetic
information
without
additional
library
preparation.
At
present,
only
a
limited
set
can
be
directly
basecalled
(for
example,
5-methylcytosine),
while
most
others
require
exploratory
methods
that
often
begin
with
alignment
nanopore
to
reference.
We
present
Uncalled4,
toolkit
for
alignment,
visualization.
Uncalled4
features
an
efficient
banded
algorithm,
BAM
file
format,
statistics
comparing
reproducible
de
novo
training
method
k-mer-based
pore
models,
revealing
potential
errors
in
Oxford
Technologies'
state-of-the-art
model.
apply
6-methyladenine
(m6A)
seven
human
cell
lines,
identifying
26%
more
than
Nanopolish
using
m6Anet,
including
several
genes
where
m6A
has
known
implications
cancer.
is
available
open
source
at
github.com/skovaka/uncalled4
.
Language: Английский
Uncalled4 improves nanopore DNA and RNA modification detection via fast and accurate signal alignment
bioRxiv (Cold Spring Harbor Laboratory),
Journal Year:
2024,
Volume and Issue:
unknown
Published: March 11, 2024
Abstract
Nanopore
signal
analysis
enables
detection
of
nucleotide
modifications
from
native
DNA
and
RNA
sequencing,
providing
both
accurate
genetic/transcriptomic
epigenetic
information
without
additional
library
preparation.
Presently,
only
a
limited
set
can
be
directly
basecalled
(e.g.
5-methylcytosine),
while
most
others
require
exploratory
methods
that
often
begin
with
alignment
nanopore
to
reference.
We
present
Uncalled4,
toolkit
for
alignment,
analysis,
visualization.
Uncalled4
features
an
efficient
banded
algorithm,
BAM
file
format,
statistics
comparing
methods,
reproducible
de
novo
training
method
k-mer-based
pore
models,
revealing
potential
errors
in
ONT’s
state-of-the-art
model.
apply
6-methyladenine
(m6A)
seven
human
cell
lines,
identifying
26%
more
than
Nanopolish
using
m6Anet,
including
several
genes
where
m6A
has
known
implications
cancer.
is
available
open-source
at
github.com/skovaka/uncalled4
.
Language: Английский
Streamlining remote nanopore data access with slow5curl
GigaScience,
Journal Year:
2024,
Volume and Issue:
13
Published: Jan. 1, 2024
Abstract
Background
As
adoption
of
nanopore
sequencing
technology
continues
to
advance,
the
need
maintain
large
volumes
raw
current
signal
data
for
reanalysis
with
updated
algorithms
is
a
growing
challenge.
Here
we
introduce
slow5curl,
software
package
designed
streamline
sharing,
accessibility,
and
reanalysis.
Results
Slow5curl
allows
user
fetch
specified
read
or
group
reads
from
dataset
stored
on
remote
server,
such
as
public
repository,
without
downloading
entire
file.
uses
an
index
quickly
specific
in
SLOW5/BLOW5
format
highly
parallelized
access
requests
maximize
download
speeds.
Using
all
Human
Pangenome
Reference
Consortium
(>22
TB),
demonstrate
how
slow5curl
can
be
used
reanalyze
corresponding
set
target
genes
each
individual
cohort
(n
=
91),
minimizing
time,
egress
costs,
local
storage
requirements
their
Conclusions
We
provide
free,
open-source
that
will
reduce
frictions
sharing
community:
https://github.com/BonsonW/slow5curl.
Language: Английский