<s>
SPAdes	B-Application
(	O
St.	O
Petersburg	O
genome	O
assembler	O
)	O
is	O
a	O
genome	O
assembly	O
algorithm	O
which	O
was	O
designed	O
for	O
single	O
cell	O
and	O
multi-cells	O
bacterial	O
data	O
sets	O
.	O
</s>
<s>
SPAdes	B-Application
works	O
with	O
Ion	O
Torrent	O
,	O
PacBio	O
,	O
Oxford	O
Nanopore	O
,	O
and	O
Illumina	O
paired-end	O
,	O
mate-pairs	O
and	O
single	O
reads	O
.	O
</s>
<s>
SPAdes	B-Application
has	O
been	O
integrated	O
into	O
Galaxy	B-Application
pipelines	O
by	O
Guy	O
Lionel	O
and	O
Philip	O
Mabon	O
.	O
</s>
<s>
Currently	O
available	O
assembler	O
,	O
such	O
as	O
Velvet	B-Application
,	O
String	O
Graph	O
Assembler	O
(	O
SGA	O
)	O
and	O
EULER-SR	O
,	O
were	O
not	O
designed	O
to	O
handle	O
SCS	O
assembly	O
.	O
</s>
<s>
Therefore	O
,	O
the	O
new	O
algorithmic	O
approach	O
,	O
SPAdes	B-Application
,	O
was	O
designed	O
to	O
address	O
these	O
issues	O
.	O
</s>
<s>
SPAdes	B-Application
uses	O
k-mers	O
for	O
building	O
the	O
initial	O
de	O
Bruijn	O
graph	O
and	O
on	O
following	O
stages	O
it	O
performs	O
graph-theoretical	O
operations	O
which	O
are	O
based	O
on	O
graph	O
structure	O
,	O
coverage	O
and	O
sequence	O
lengths	O
.	O
</s>
<s>
The	O
stages	O
of	O
assembly	O
in	O
SPAdes	B-Application
are	O
:	O
</s>
<s>
SPAdes	B-Application
employs	O
multisized	O
de	O
Bruijn	O
graph	O
(	O
See	O
below	O
)	O
,	O
which	O
detects	O
and	O
removes	O
bulge/bubble	O
and	O
chimeric	O
reads	O
.	O
</s>
<s>
SPAdes	B-Application
outputs	O
contigs	O
and	O
allows	O
to	O
map	O
reads	O
back	O
to	O
their	O
positions	O
in	O
the	O
assembly	O
graph	O
after	O
graph	O
simplification	O
(	O
backtracking	O
)	O
.	O
</s>
<s>
SPAdes	B-Application
was	O
designed	O
to	O
overcome	O
the	O
problems	O
associated	O
with	O
the	O
assembly	O
of	O
single	O
cell	O
data	O
as	O
follows	O
:	O
</s>
<s>
SPAdes	B-Application
utilizes	O
multisized	O
de	O
Bruijn	O
graph	O
which	O
allows	O
employing	O
different	O
values	O
of	O
k	O
.	O
It	O
has	O
been	O
suggested	O
to	O
use	O
smaller	O
values	O
of	O
k	O
in	O
low-coverage	O
regions	O
to	O
minimize	O
fragmentation	O
,	O
and	O
larger	O
values	O
of	O
k	O
in	O
high	O
coverage	O
regions	O
to	O
decrease	O
repeat	O
collapsing	O
(	O
Stage	O
1	O
above	O
)	O
.	O
</s>
<s>
SPAdes	B-Application
employs	O
the	O
basic	O
concept	O
of	O
paired	O
de	O
Bruijn	O
graphs	O
.	O
</s>
<s>
Therefore	O
,	O
SPAdes	B-Application
estimates	O
'	O
distances	O
 '	O
instead	O
of	O
using	O
'	O
insert	O
sizes	O
 '	O
.	O
</s>
<s>
To	O
construct	O
paired	O
de	O
Bruijn	O
graph	O
,	O
the	O
rectangle	O
graphs	O
are	O
employed	O
in	O
SPAdes	B-Application
(	O
stage	O
3	O
)	O
.	O
</s>
<s>
SPAdes	B-Application
identifies	O
these	O
based	O
on	O
graph	O
topology	O
,	O
the	O
length	O
and	O
coverage	O
of	O
the	O
non-branching	O
paths	O
included	O
in	O
them	O
.	O
</s>
<s>
SPAdes	B-Application
keeps	O
a	O
data	O
structure	O
to	O
be	O
able	O
to	O
backtrack	O
all	O
corrections	O
or	O
removals	O
.	O
</s>
<s>
SPAdes	B-Application
modifies	O
the	O
previously	O
used	O
bulge	O
removal	O
approach	O
and	O
iterative	B-Algorithm
de	O
Bruijn	O
graph	O
approach	O
from	O
Peng	O
et	O
al	O
(	O
2010	O
)	O
and	O
creates	O
a	O
new	O
approach	O
called	O
‘‘	O
bulge	O
corremoval’’	O
,	O
which	O
stands	O
for	O
bulge	O
correction	O
and	O
removal	O
.	O
</s>
<s>
If	O
P	O
is	O
a	O
non-branching	O
path	O
(	O
h-path	O
)	O
,	O
then	O
SPAdes	B-Application
maps	O
every	O
edge	O
in	O
P	O
to	O
an	O
edge	O
projection	O
in	O
Q	O
and	O
removes	O
P	O
from	O
the	O
graph	O
,	O
as	O
a	O
result	O
the	O
coverage	O
of	O
Q	O
increases	O
.	O
</s>
<s>
Unlike	O
other	O
assemblers	O
,	O
which	O
use	O
a	O
fixed	O
coverage	O
cut-off	O
bulge	O
removal	O
,	O
SPAdes	B-Application
removes	O
or	O
projects	O
the	O
h-paths	O
with	O
low	O
coverage	O
step	O
by	O
step	O
.	O
</s>
<s>
Moreover	O
,	O
in	O
order	O
to	O
guarantee	O
that	O
no	O
new	O
sources/sinks	O
are	O
introduced	O
to	O
the	O
graph	O
,	O
SPAdes	B-Application
deletes	O
an	O
h-path	O
(	O
in	O
chimeric	O
h-path	O
removal	O
)	O
or	O
projects	O
(	O
in	O
bulge	O
corremoval	O
)	O
only	O
if	O
its	O
start	O
and	O
end	O
vertices	O
have	O
at	O
least	O
two	O
outgoing	O
and	O
ingoing	O
edges	O
.	O
</s>
<s>
SPAdes	B-Application
is	O
composed	O
of	O
the	O
following	O
tools	O
:	O
</s>
<s>
Iterative	B-Algorithm
short-read	O
genome	O
assembler	O
,	O
SPAdes	B-Application
.	O
</s>
<s>
It	O
takes	O
~	O
40%	O
of	O
this	O
time	O
to	O
perform	O
stage	O
1	O
(	O
see	O
SPAdes	B-Application
assembly	O
approach	O
above	O
)	O
when	O
using	O
three	O
iterations	B-Algorithm
(	O
k	O
=	O
22	O
,	O
34	O
and	O
56	O
)	O
,	O
and	O
~	O
45%	O
,	O
14%	O
and	O
1%	O
for	O
completing	O
stages	O
2	O
,	O
3	O
and	O
4	O
,	O
respectively	O
.	O
</s>
<s>
Mismatch	O
corrector	O
(	O
which	O
uses	O
the	O
BWA	B-Application
tool	O
)	O
.	O
</s>
<s>
These	O
assemblers	O
are	O
EULER-SR	O
,	O
Velvet	B-Application
,	O
SOAPdenovo	O
,	O
Velvet-SC	O
,	O
EULER+	O
Velvet-SC	O
(	O
E+	O
V-SC	O
)	O
,	O
IDBA-UD	O
and	O
SPAdes	B-Application
.	O
</s>
<s>
It	O
was	O
demonstrated	O
that	O
IDBA-UD	O
and	O
SPAdes	B-Application
performed	O
the	O
best	O
.	O
</s>
<s>
SPAdes	B-Application
had	O
the	O
largest	O
NG50	O
(	O
99	O
,	O
913	O
,	O
NG50	O
statistics	O
is	O
the	O
same	O
as	O
the	O
N50	O
except	O
that	O
the	O
genome	O
size	O
is	O
used	O
rather	O
than	O
the	O
assembly	O
size	O
)	O
.	O
</s>
<s>
Moreover	O
,	O
using	O
E	O
.	O
coli	O
reference	O
genome	O
,	O
SPAdes	B-Application
assembled	O
the	O
highest	O
percentage	O
of	O
genome	O
(	O
97%	O
)	O
and	O
the	O
highest	O
number	O
of	O
complete	O
genes	O
(	O
4,071	O
out	O
of	O
4,324	O
)	O
.	O
</s>
