Genome Research,
Journal Year:
2017,
Volume and Issue:
27(5), P. 885 - 896
Published: April 18, 2017
Advances
in
genome
sequencing
and
assembly
technologies
are
generating
many
high-quality
sequences,
but
assemblies
of
large,
repeat-rich
polyploid
genomes,
such
as
that
bread
wheat,
remain
fragmented
incomplete.
We
have
generated
a
new
wheat
whole-genome
shotgun
sequence
using
combination
optimized
data
types
an
algorithm
designed
to
deal
with
large
complex
genomes.
The
represents
>78%
the
scaffold
N50
88.8
kb
has
high
fidelity
input
data.
Our
annotation
combines
strand-specific
Illumina
RNA-seq
Pacific
Biosciences
(PacBio)
full-length
cDNAs
identify
104,091
high-confidence
protein-coding
genes
10,156
noncoding
RNA
genes.
confirmed
three
known
identified
one
novel
rearrangements.
approach
enables
rapid
scalable
identification
structural
variants,
definition
complete
gene
models,
all
powerful
resources
for
trait
analysis
breeding
this
key
global
crop.
Genome biology,
Journal Year:
2013,
Volume and Issue:
14(5)
Published: May 27, 2013
Abstract
Methods
to
reliably
assess
the
accuracy
of
genome
sequence
data
are
lacking.
Currently
completeness
is
only
described
qualitatively
and
mis-assemblies
overlooked.
Here
we
present
REAPR,
a
tool
that
precisely
identifies
errors
in
assemblies
without
need
for
reference
sequence.
We
have
validated
REAPR
on
complete
genomes
or
de
novo
from
bacteria,
malaria
Caenorhabditis
elegans
,
demonstrate
86%
82%
human
mouse
error-free,
respectively.
When
applied
an
ongoing
project,
provides
corrected
assembly
statistics
allowing
quantitative
comparison
multiple
assemblies.
available
at
http://www.sanger.ac.uk/resources/software/reapr/
.
Briefings in Bioinformatics,
Journal Year:
2019,
Volume and Issue:
22(1), P. 178 - 193
Published: Nov. 7, 2019
Analyzing
the
microbiome
of
diverse
species
and
environments
using
next-generation
sequencing
techniques
has
significantly
enhanced
our
understanding
on
metabolic,
physiological
ecological
roles
environmental
microorganisms.
However,
analysis
is
affected
by
experimental
conditions
(e.g.
errors
genomic
repeats)
computationally
intensive
cumbersome
downstream
quality
control,
assembly,
binning
statistical
analyses).
Moreover,
introduction
new
technologies
protocols
led
to
a
flood
methodologies,
which
also
have
an
immediate
effect
results
analyses.
The
aim
this
work
review
most
important
workflows
for
16S
rRNA
shotgun
long-read
metagenomics,
as
well
provide
best-practice
design,
sample
processing,
sequencing,
binning,
annotation
visualization.
To
simplify
standardize
computational
analysis,
we
set
metagenomic
data
(available
at
https://github.com/grimmlab/MicrobiomeBestPracticeReview).
Genome Research,
Journal Year:
2017,
Volume and Issue:
27(5), P. 885 - 896
Published: April 18, 2017
Advances
in
genome
sequencing
and
assembly
technologies
are
generating
many
high-quality
sequences,
but
assemblies
of
large,
repeat-rich
polyploid
genomes,
such
as
that
bread
wheat,
remain
fragmented
incomplete.
We
have
generated
a
new
wheat
whole-genome
shotgun
sequence
using
combination
optimized
data
types
an
algorithm
designed
to
deal
with
large
complex
genomes.
The
represents
>78%
the
scaffold
N50
88.8
kb
has
high
fidelity
input
data.
Our
annotation
combines
strand-specific
Illumina
RNA-seq
Pacific
Biosciences
(PacBio)
full-length
cDNAs
identify
104,091
high-confidence
protein-coding
genes
10,156
noncoding
RNA
genes.
confirmed
three
known
identified
one
novel
rearrangements.
approach
enables
rapid
scalable
identification
structural
variants,
definition
complete
gene
models,
all
powerful
resources
for
trait
analysis
breeding
this
key
global
crop.
