<s>
SOAP	B-Application
(	O
Short	B-Application
Oligonucleotide	I-Application
Analysis	I-Application
Package	I-Application
)	O
is	O
a	O
suite	O
of	O
bioinformatics	O
software	O
tools	O
from	O
the	O
BGI	O
Bioinformatics	O
department	O
enabling	O
the	O
assembly	O
,	O
alignment	O
,	O
and	O
analysis	O
of	O
next	O
generation	O
DNA	O
sequencing	O
data	O
.	O
</s>
<s>
All	O
programs	O
in	O
the	O
SOAP	B-Application
package	O
may	O
be	O
used	O
free	O
of	O
charge	O
and	O
are	O
distributed	O
under	O
the	O
GPL	B-License
open	B-Application
source	I-Application
software	I-Application
license	O
.	O
</s>
<s>
The	O
SOAP	B-Application
suite	O
of	O
tools	O
can	O
be	O
used	O
to	O
perform	O
the	O
following	O
genome	O
assembly	O
tasks	O
:	O
</s>
<s>
SOAPaligner	O
(	O
SOAP2	O
)	O
is	O
specifically	O
designed	O
for	O
fast	O
alignment	O
of	O
short	O
reads	O
and	O
performs	O
favorably	O
with	O
respect	O
to	O
similar	O
alignment	O
tools	O
such	O
as	O
Bowtie	B-Application
and	O
MAQ	O
.	O
</s>
<s>
The	O
first	O
release	O
of	O
SOAP	B-Application
consisted	O
only	O
of	O
the	O
sequence	B-Algorithm
alignment	I-Algorithm
tool	O
SOAPaligner	O
.	O
</s>
<s>
SOAP	B-Application
v2	O
extended	O
and	O
improved	O
on	O
SOAP	B-Application
v1	O
by	O
significantly	O
improving	O
the	O
performance	O
of	O
the	O
SOAPaligner	O
tool	O
.	O
</s>
<s>
The	O
SOAP	B-Application
suite	O
was	O
expanded	O
then	O
to	O
include	O
the	O
new	O
tools	O
:	O
SOAPdenovo	O
1&2	O
,	O
SOAPindel	O
,	O
SOAPsnp	O
,	O
and	O
SOAPsv	O
.	O
</s>
<s>
SOAP	B-Application
v3	O
extended	O
the	O
alignment	O
tool	O
by	O
being	O
the	O
first	O
short-read	O
alignment	O
tool	O
to	O
utilize	O
GPU	O
processors	O
.	O
</s>
<s>
As	O
a	O
result	O
of	O
these	O
improvements	O
,	O
SOAPalign	O
significantly	O
outperformed	O
competing	O
aligners	O
Bowtie	B-Application
and	O
BWA	O
in	O
terms	O
of	O
speed	O
.	O
</s>
