<s>
Velvet	B-Application
is	O
an	O
algorithm	O
package	O
that	O
has	O
been	O
designed	O
to	O
deal	O
with	O
de	O
novo	O
genome	O
assembly	O
and	O
short	O
read	O
sequencing	B-Algorithm
alignments	I-Algorithm
.	O
</s>
<s>
Velvet	B-Application
has	O
also	O
been	O
implemented	O
in	O
commercial	O
packages	O
,	O
such	O
as	O
Sequencher	O
,	O
Geneious	O
,	O
MacVector	B-Application
and	O
BioNumerics	B-Application
.	O
</s>
<s>
This	O
led	O
to	O
the	O
development	O
of	O
Velvet	B-Application
by	O
Daniel	O
Zerbino	O
and	O
Ewan	O
Birney	O
at	O
the	O
European	O
Bioinformatics	O
Institute	O
in	O
the	O
United	O
Kingdom	O
.	O
</s>
<s>
Velvet	B-Application
works	O
by	O
efficiently	O
manipulating	O
de	O
Bruijn	O
graphs	O
through	O
simplification	O
and	O
compression	O
,	O
without	O
the	O
loss	O
of	O
graph	O
information	O
,	O
by	O
converging	O
non-intersecting	O
paths	O
into	O
single	O
nodes	O
.	O
</s>
<s>
The	O
combination	O
of	O
short	O
reads	O
and	O
read	O
pairs	O
allows	O
Velvet	B-Application
to	O
resolve	O
small	O
repeats	O
and	O
produce	O
contigs	B-Application
of	O
reasonable	O
length	O
.	O
</s>
<s>
This	O
application	O
of	O
Velvet	B-Application
can	O
produce	O
contigs	B-Application
with	O
a	O
N50	O
length	O
of	O
50	O
kb	O
on	O
paired-end	O
prokaryotic	O
data	O
and	O
a	O
3	O
kb	O
length	O
for	O
regions	O
of	O
mammalian	O
data	O
.	O
</s>
<s>
As	O
already	O
mentioned	O
Velvet	B-Application
uses	O
the	O
de	O
Bruijn	O
graph	O
to	O
assemble	O
short	O
reads	O
.	O
</s>
<s>
More	O
specifically	O
Velvet	B-Application
represents	O
each	O
different	O
k-mer	O
obtained	O
from	O
the	O
reads	O
by	O
a	O
unique	O
node	O
on	O
the	O
graph	O
.	O
</s>
<s>
The	O
following	O
figure	O
shows	O
an	O
example	O
of	O
a	O
de	O
Bruijn	O
graph	O
generated	O
with	O
Velvet	B-Application
:	O
</s>
<s>
Velvet	B-Application
recognizes	O
three	O
kinds	O
of	O
errors	O
:	O
tips	O
;	O
bubbles	O
;	O
and	O
erroneous	O
connections	O
.	O
</s>
<s>
These	O
errors	O
are	O
removed	O
using	O
the	O
Tour	O
Bus	O
algorithm	O
,	O
which	O
is	O
similar	O
to	O
a	O
Dijkstra	B-Algorithm
's	I-Algorithm
algorithm	I-Algorithm
,	O
a	O
breadth-first	B-Algorithm
search	I-Algorithm
that	O
detects	O
the	O
best	O
path	O
to	O
follow	O
and	O
determines	O
which	O
ones	O
should	O
be	O
erased	O
.	O
</s>
<s>
Velvet	B-Application
erases	O
these	O
errors	O
after	O
completion	O
of	O
the	O
Tour	O
Bus	O
algorithm	O
,	O
applying	O
a	O
simple	O
coverage	O
cut-off	O
that	O
must	O
be	O
defined	O
by	O
the	O
user	O
.	O
</s>
<s>
Velvet	B-Application
provides	O
the	O
following	O
functions	O
:	O
</s>
<s>
It	O
then	O
extracts	O
the	O
contigs	B-Application
.	O
</s>
<s>
Most	O
importantly	O
,	O
a	O
file	O
of	O
contigs	B-Application
contains	O
the	O
sequences	O
of	O
the	O
contigs	B-Application
longer	O
than	O
2k	O
,	O
where	O
k	O
is	O
the	O
word-length	O
used	O
in	O
velveth	O
.	O
</s>
<s>
Velvet	B-Application
algorithms	O
was	O
designed	O
for	O
this	O
and	O
are	O
able	O
to	O
perform	O
short	O
read	O
de	O
novo	O
sequencing	O
alignment	O
in	O
relatively	O
short	O
computational	O
time	O
and	O
with	O
lower	O
memory	O
usage	O
compared	O
to	O
other	O
assemblers	O
.	O
</s>
<s>
One	O
of	O
the	O
main	O
drawbacks	O
in	O
the	O
use	O
of	O
Velvet	B-Application
is	O
the	O
use	O
of	O
the	O
command-line	O
interface	O
and	O
the	O
difficulties	O
users	O
,	O
especially	O
beginners	O
,	O
face	O
in	O
the	O
implementation	O
of	O
their	O
data	O
.	O
</s>
<s>
A	O
graphical	O
user	O
interface	O
for	O
the	O
Velvet	B-Application
assembler	I-Application
was	O
developed	O
in	O
2012	O
and	O
designed	O
to	O
overcome	O
this	O
problem	O
and	O
simplify	O
the	O
running	O
of	O
Velvet	B-Application
.	O
</s>
