<s>
Bowtie	B-Application
is	O
a	O
software	O
package	O
commonly	O
used	O
for	O
sequence	B-Algorithm
alignment	I-Algorithm
and	O
sequence	O
analysis	O
in	O
bioinformatics	O
.	O
</s>
<s>
The	O
source	O
code	O
for	O
the	O
package	O
is	O
distributed	O
freely	B-Application
and	O
compiled	O
binaries	O
are	O
available	O
for	O
Linux	B-Application
,	O
macOS	B-Application
and	O
Windows	O
platforms	O
.	O
</s>
<s>
As	O
of	O
2017	O
,	O
the	O
Genome	O
Biology	O
paper	O
describing	O
the	O
original	O
Bowtie	B-Application
method	O
has	O
been	O
cited	O
more	O
than	O
11,000	O
times	O
.	O
</s>
<s>
Bowtie	B-Application
is	O
open-source	B-Application
software	I-Application
and	O
is	O
currently	O
maintained	O
by	O
Johns	O
Hopkins	O
University	O
.	O
</s>
<s>
The	O
Bowtie	B-Application
sequence	O
aligner	O
was	O
originally	O
developed	O
by	O
Ben	O
Langmead	O
et	O
al	O
.	O
</s>
<s>
Bowtie	B-Application
is	O
promoted	O
as	O
"	O
an	O
ultrafast	O
,	O
memory-efficient	O
short	O
aligner	O
for	O
short	O
DNA	O
sequences.	O
"	O
</s>
<s>
The	O
speed	O
increase	O
of	O
Bowtie	B-Application
is	O
partly	O
due	O
to	O
implementing	O
the	O
Burrows	B-Algorithm
–	I-Algorithm
Wheeler	I-Algorithm
transform	I-Algorithm
for	O
aligning	O
,	O
which	O
reduces	O
the	O
memory	O
footprint	O
(	O
typically	O
to	O
around	O
2.2GB	O
for	O
the	O
human	O
genome	O
)	O
;	O
a	O
similar	O
method	O
is	O
used	O
by	O
the	O
BWA	O
and	O
SOAP2	B-Application
alignment	O
methods	O
.	O
</s>
<s>
Bowtie	B-Application
conducts	O
a	O
quality-aware	O
,	O
greedy	O
,	O
randomized	O
,	O
depth-first	B-Algorithm
search	I-Algorithm
through	O
the	O
space	O
of	O
possible	O
alignments	O
.	O
</s>
<s>
Because	O
the	O
search	O
is	O
greedy	O
,	O
the	O
first	O
valid	O
alignment	O
encountered	O
by	O
Bowtie	B-Application
will	O
not	O
necessarily	O
be	O
the	O
'	O
best	O
 '	O
in	O
terms	O
of	O
the	O
number	O
of	O
mismatches	O
or	O
in	O
terms	O
of	O
quality	O
.	O
</s>
<s>
Bowtie	B-Application
is	O
used	O
as	O
a	O
sequence	O
aligner	O
by	O
a	O
number	O
of	O
other	O
related	O
bioinformatics	O
algorithms	O
,	O
including	O
TopHat	B-Application
,	O
Cufflinks	O
and	O
the	O
CummeRbund	O
Bioconductor	B-Application
package	O
.	O
</s>
<s>
On	O
16	O
October	O
2011	O
,	O
the	O
developers	O
released	O
a	O
beta	O
fork	B-Application
of	O
the	O
project	O
called	O
Bowtie	B-Application
2	O
.	O
</s>
<s>
In	O
addition	O
to	O
the	O
Burrows-Wheeler	B-Algorithm
transform	I-Algorithm
,	O
Bowtie	B-Application
2	O
also	O
uses	O
an	O
FM-index	B-Algorithm
(	O
similar	O
to	O
a	O
suffix	B-Algorithm
array	I-Algorithm
)	O
to	O
keep	O
its	O
memory	O
footprint	O
small	O
.	O
</s>
<s>
Due	O
to	O
its	O
implementation	O
,	O
Bowtie	B-Application
2	O
is	O
more	O
suited	O
to	O
finding	O
longer	O
,	O
gapped	O
alignments	O
in	O
comparison	O
with	O
the	O
original	O
Bowtie	B-Application
method	O
.	O
</s>
<s>
There	O
is	O
no	O
upper	O
limit	O
on	O
read	O
length	O
in	O
Bowtie	B-Application
2	O
and	O
it	O
allows	O
alignments	O
to	O
overlap	O
ambiguous	O
characters	O
in	O
the	O
reference	O
.	O
</s>
