<s>
De	B-Application
novo	I-Application
sequence	I-Application
assemblers	I-Application
are	O
a	O
type	O
of	O
program	O
that	O
assembles	O
short	O
nucleotide	O
sequences	O
into	O
longer	O
ones	O
without	O
the	O
use	O
of	O
a	O
reference	O
genome	O
.	O
</s>
<s>
Two	O
common	O
types	O
of	O
de	O
novo	O
assemblers	O
are	O
greedy	B-Algorithm
algorithm	I-Algorithm
assemblers	O
and	O
De	O
Bruijn	O
graph	O
assemblers	O
.	O
</s>
<s>
There	O
are	O
two	O
types	O
of	O
algorithms	O
that	O
are	O
commonly	O
utilized	O
by	O
these	O
assemblers	O
:	O
greedy	B-Algorithm
,	O
which	O
aim	O
for	O
local	O
optima	O
,	O
and	O
graph	O
method	O
algorithms	O
,	O
which	O
aim	O
for	O
global	O
optima	O
.	O
</s>
<s>
Greedy	B-Algorithm
algorithm	I-Algorithm
assemblers	O
are	O
assemblers	O
that	O
find	O
local	O
optima	O
in	O
alignments	O
of	O
smaller	O
reads	O
.	O
</s>
<s>
Greedy	B-Algorithm
algorithm	I-Algorithm
assemblers	O
typically	O
feature	O
several	O
steps	O
:	O
1	O
)	O
pairwise	O
distance	O
calculation	O
of	O
reads	O
,	O
2	O
)	O
clustering	O
of	O
reads	O
with	O
greatest	O
overlap	O
,	O
3	O
)	O
assembly	O
of	O
overlapping	O
reads	O
into	O
larger	O
contigs	B-Application
,	O
and	O
4	O
)	O
repeat	O
.	O
</s>
<s>
Early	O
de	B-Application
novo	I-Application
sequence	I-Application
assemblers	I-Application
,	O
such	O
as	O
SEQAID	O
(	O
1984	O
)	O
and	O
CAP	O
(	O
1992	O
)	O
,	O
used	O
greedy	B-Algorithm
algorithms	I-Algorithm
,	O
such	O
as	O
overlap-layout-consensus	O
(	O
OLC	O
)	O
algorithms	O
.	O
</s>
<s>
De	O
Bruijn	O
graph	O
assemblers	O
typically	O
perform	O
better	O
on	O
larger	O
read	O
sets	O
than	O
greedy	B-Algorithm
algorithm	I-Algorithm
assemblers	O
(	O
especially	O
when	O
they	O
contain	O
repeat	O
regions	O
)	O
.	O
</s>
<s>
Illumina	O
,	O
ABI	O
SOLiD	O
,	O
Roche	O
454	O
,	O
Ion	O
Torrent	O
,	O
Solexa	O
,	O
Sanger	O
DNASTAR	O
2007	O
/	O
2023	O
C	O
link	O
Newbler	B-Application
genomes	O
,	O
ESTs	O
454	O
,	O
Sanger	O
454	O
Life	O
Sciences	O
2004/2012	O
C	O
link	O
Phrap	B-Application
genomes	O
Sanger	O
,	O
454	O
,	O
Solexa	O
Green	O
,	O
P	O
.	O
1994	O
/	O
2008	O
C	O
/	O
NC-A	O
link	O
Plass	O
Protein-level	O
assembler	O
:	O
assembles	O
six-frame-translated	O
sequencing	O
reads	O
into	O
protein	O
sequences	O
Illumina	O
2018	O
/	O
2019	O
OS	O
linkRaya	O
suite	O
of	O
assemblers	O
including	O
de	O
novo	O
,	O
metagenomic	O
,	O
ontology	O
and	O
taxonomic	O
profiling	O
;	O
uses	O
a	O
De	O
Bruijn	O
graph2010OSlink	O
SPAdes	B-Application
(	O
small	O
)	O
genomes	O
,	O
single-cell	O
Illumina	O
,	O
Solexa	O
,	O
Sanger	O
,	O
454	O
,	O
Ion	O
Torrent	O
,	O
PacBio	O
,	O
Oxford	O
Nanopore	O
2012	O
/	O
2021	O
OS	O
link	O
Velvet	B-Application
(	O
small	O
)	O
genomes	O
Sanger	O
,	O
454	O
,	O
Solexa	O
,	O
SOLiD	O
2007	O
/	O
2011	O
OS	O
linkHGAPGenomes	O
up	O
to	O
130	O
MBPacBio	O
readsChin	O
,	O
Chen-Shan	O
,	O
David	O
H	O
.	O
Alexander	O
,	O
Patrick	O
Marks	O
,	O
Aaron	O
A	O
.	O
Klammer	O
,	O
James	O
Drake	O
,	O
Cheryl	O
Heiner	O
,	O
Alicia	O
Clum	O
et	O
al	O
.	O
</s>
<s>
Overall	O
:	O
Overall	O
,	O
the	O
Baylor	O
College	O
of	O
Medicine	O
Human	O
Genome	O
Sequencing	O
Center	O
utilizing	O
a	O
variety	O
of	O
assembly	O
methods	O
(	O
SeqPrep	O
,	O
KmerFreq	O
,	O
Quake	O
,	O
BWA	O
,	O
Newbler	B-Application
,	O
ALLPATHS-LG	O
,	O
Atlas-Link	O
,	O
Atlas-GapFill	O
,	O
Phrap	B-Application
,	O
CrossMatch	O
,	O
Velvet	B-Application
,	O
BLAST	O
,	O
and	O
BLASR	O
)	O
performed	O
the	O
best	O
for	O
the	O
bird	O
and	O
fish	O
assemblies	O
.	O
</s>
