<s>
TopHat	B-Application
is	O
an	O
open-source	O
bioinformatics	O
tool	O
for	O
the	O
throughput	O
alignment	O
of	O
shotgun	O
cDNA	O
sequencing	O
reads	O
generated	O
by	O
transcriptomics	O
technologies	O
(	O
e.g.	O
</s>
<s>
RNA-Seq	O
)	O
using	O
Bowtie	B-Application
first	O
and	O
then	O
mapping	O
to	O
a	O
reference	O
genome	O
to	O
discover	O
RNA	O
splice	O
sites	O
de	O
novo	O
.	O
</s>
<s>
TopHat	B-Application
aligns	O
RNA-Seq	O
reads	O
to	O
mammalian-sized	O
genomes	O
.	O
</s>
<s>
TopHat	B-Application
was	O
originally	O
developed	O
in	O
2009	O
by	O
Cole	O
Trapnell	O
,	O
Lior	O
Pachter	O
and	O
Steven	O
Salzberg	O
at	O
the	O
Center	O
for	O
Bioinformatics	O
and	O
Computational	O
Biology	O
at	O
the	O
University	O
of	O
Maryland	O
,	O
College	O
Park	O
and	O
at	O
the	O
Mathematics	O
Department	O
,	O
UC	O
Berkeley	O
.	O
</s>
<s>
Kim	O
re-wrote	O
some	O
of	O
Trapnell	O
's	O
original	O
TopHat	B-Application
code	O
in	O
C++	B-Language
to	O
make	O
it	O
much	O
faster	O
,	O
and	O
added	O
many	O
heuristics	O
to	O
improve	O
its	O
accuracy	O
,	O
in	O
a	O
collaboration	O
with	O
Cole	O
Trapnell	O
and	O
others	O
.	O
</s>
<s>
Kim	O
and	O
Salzberg	O
also	O
developed	O
TopHat-fusion	O
which	O
used	O
transcriptome	O
data	O
to	O
discover	O
gene	O
fusions	O
in	O
cancer	O
tissues	O
.	O
</s>
<s>
TopHat	B-Application
is	O
used	O
to	O
align	O
reads	O
from	O
an	O
RNA-Seq	O
experiment	O
.	O
</s>
<s>
TopHat	B-Application
can	O
be	O
used	O
with	O
the	O
Tuxedo	B-Application
pipeline	O
,	O
and	O
is	O
frequently	O
used	O
with	O
Bowtie	B-Application
.	O
</s>
<s>
When	O
TopHat	B-Application
first	O
came	O
out	O
,	O
it	O
was	O
faster	O
than	O
previous	O
systems	O
.	O
</s>
<s>
Tophat	B-Application
uses	O
Bowtie	B-Application
in	O
the	O
beginning	O
to	O
analyze	O
the	O
reads	O
,	O
but	O
then	O
does	O
more	O
to	O
analyze	O
the	O
reads	O
that	O
span	O
exon-exon	O
junctions	O
.	O
</s>
<s>
If	O
you	O
are	O
using	O
TopHat	B-Application
for	O
RNA-Seq	O
data	O
,	O
you	O
will	O
get	O
more	O
read	O
aligned	O
against	O
the	O
reference	O
genome	O
.	O
</s>
<s>
Another	O
advantage	O
for	O
TopHat	B-Application
is	O
that	O
it	O
does	O
not	O
need	O
to	O
rely	O
on	O
known	O
splice	O
sites	O
when	O
aligning	O
reads	O
to	O
a	O
reference	O
genome	O
.	O
</s>
<s>
TopHat	B-Application
is	O
in	O
a	O
low	O
maintenance	O
,	O
low	O
support	O
stage	O
,	O
and	O
contains	O
software	O
bugs	O
that	O
have	O
spawned	O
3rd	O
party	O
post-processing	O
software	O
to	O
correct	O
.	O
</s>
