Finished bacterial genomes from shotgun
Filipe J. Ribeiro,1,2Dariusz Przybylski,1Shuangye Yin, Ted Sharpe, Sante Gnerre,
Amr Abouelleil, Aaron M. Berlin, Anna Montmayeur, Terrance P. Shea, Bruce J. Walker,
Sarah K. Young, Carsten Russ, Chad Nusbaum, Iain MacCallum, and David B. Jaffe3
Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
Exceptionally accurate genome reference sequences have proven to be of great value to microbial researchers. Thus, to
date, about 1800 bacterial genome assemblies have been ‘‘finished’’ at great expense with the aid of manual laboratory
and computational processes that typically iterate over a period of months or even years. By applying a new laboratory
design and new assembly algorithm to 16 samples, we demonstrate that assemblies exceeding finished quality can be
obtained from whole-genome shotgun data and automated computation. Cost and time requirements are thus dra-
[Supplemental material is available for this article.]
to microbial biology. Once thought to be impossible, de novo as-
sembly of short, massively parallel sequencing data is now com-
mon practice, with several tools now available (e.g., Chaisson and
Pevzner 2008; Zerbino and Birney 2008; MacCallum et al. 2009;
Simpson et al. 2009; Li et al. 2010; Chapman et al. 2011; Gnerre
et al. 2011; Simpson and Durbin 2012). Standard automated
methods have yielded genome assemblies that are generally of
good quality, and in a few cases, with some manual work, near-
complete genomes have been achieved (Nagarajan et al. 2010;
Rasko et al. 2011a). However, most assemblies have had many er-
rors and gaps, both in the era of Sanger sequencing (Fraser et al.
2002) and in the current short read era (Klassen and Currie 2012).
Importantly, the most difficult (e.g., rapidly evolving) regions are
often absent or incorrectly rendered. Fortunately, bacteria have
small genomes (generally 2–6 Mb), and thus in many cases, it has
been feasible to expend extra effort to determine their sequences
correctly. Indeed, to date, about 1800 bacterial genome assem-
blies (Genomes Online Database; http://www.genomesonline.org)
involving a combination of manual laboratory and computational
processes (Chain et al. 2009). These processes are applied itera-
tively and are thus slow and expensive. There remains a need for
new methods that are both faster and more economical.
To that end, in this study, we define a new recipe for whole-
genome shotgun sequencing and a new algorithm to assemble
such data, incorporated as part of the program ALLPATHS-LG
(MacCallum et al. 2009). The recipe uses a mixture of three data
types generated using sequencing technology from two vendors,
Illumina (Bentley et al. 2008) and Pacific Biosciences (Eid et al.
2009), that together span a broad range in their resolving power.
These technologies are complementary and, at least theoretically,
provide the capability of accurately assembling the entire genome.
All of the laboratory and computational methods are essentially
automated, thus reducing costs and keeping project turnaround
time to a minimum.
We apply these methods to 16 bacterial samples, three of which
were previously finished, thus functioning as controls for our
work. We applied the same laboratory methods and identical
(pushbutton) computations to each of the resulting data sets. We
describetheresulting assemblies (completecircles in severalcases),
and for those having the finished reference sequences are able to
assess the accuracy both of our assemblies and the finished refer-
We reasoned that creation of optimal assemblies would require
would need to be synchronized. For our formula, we settled on
three data types and approximate levels of coverage that could
facilitate generation of assemblies of exceptionally high quality
size range, these data are (A) short fragment read pairs from Illu-
mina, (B) long reads from Pacific Biosciences, and (C) jumping
pairs from Illumina with a wide size range.
These data have complementary attributes. Thus, Illumina
data have high base accuracy, compensating for the relatively
low accuracy of the Pacific Biosciences data (Eid et al. 2009).
Conversely, the Pacific Biosciences data are generated without
amplification and thus could provide coverage in regions that are
underrepresented or absent in Illumina data due to amplification
bias in the sample preparation. Finally, the data are spread across
three size ranges. In particular, we note that because the jumping
pairs are created from a wide size range of material, they can span
considerable distances (5 kb or more). However, there is a trade-
off because a tight size range would give greater accuracy to dis-
1These authors contributed equally to this work.
2Present address: New York Genome Center, 590 Madison Avenue,
New York, NY 10022, USA.
Article published online before print. Article, supplemental material, and pub-
lication date are at http://www.genome.org/cgi/doi/10.1101/gr.141515.112.
Freely available online through the Genome Research Open Access option.
2270 Genome Research
22:2270–2277 ? 2012, Published by Cold Spring Harbor Laboratory Press; ISSN 1088-9051/12; www.genome.org
tinguish shorter distances. Fortunately, the Pacific Biosciences
reads are effective in the middle distance range where the jumps
data types with respect to accuracy, bias, and resolution range. In
steps (for more detail, see Supplemental Methods; for explanatory
diagrams, see Fig. 1):
Step I: Build unipaths using a minimum overlap of K = 96
which can be formally described in terms of the de Bruijn graph.
Informally a ‘‘unipath’’ is a maximal unbranched sequence in the
genome, relative to the given K (Butler et al. 2008), so that the
perfect unipath graph for the genome could be obtained from it by
graph could be obtained from a collection of perfect reads of
length > K, at high enough depth so that all K-base overlaps are
represented. An approximation to the perfect unipath graph can
Laboratory formula for finished genome assembly
Size of input
A 0.16–0.22 Paired reads from
Accurate, resolves short-range repeats
B 1–3 Pacific Biosciences1000 503
Relatively unbiased, resolves
Resolves long-range repeatsC 2–10Paired reads from jumps Illumina100 503
aType is one of three data types, A, B, or C.
bSize of input material (kb) is the approximate size range of the input DNA.
cConstruct is the molecular biology construction from the input DNA.
dSequencing platform is the technology brand on which data were generated.
eRead length (bases) is the target read length (approximate average for Pacific Biosciences reads).
fCoverage (3) is the approximate fold coverage of the genome to be generated. Coverage is computed based on all reads, passing or not; however for
Illumina reads, we count only Q20 bases in such reads, and for Pacific Biosciences reads, we count only bases lying in the aligning portion of a given read.
gAdvantages are the reasons this data type could improve assembly quality.
copies of size K are ‘glued together.’ In the figure, this happens to two copies of a repeat R. (Unipath graphs are actually directed, and both strands of the
we construct an approximation to the ideal unipath graph. First, individual fragment read pairs are ‘closed’ by recruiting a third read (red; from some other
pair). Then the resulting ‘super-reads’ are glued together along perfect repeats of size $K. We use K = 96, about half the fragment size. Primarily because of
reads are unrolled along unipath graph as in main text Step II.1. (Top) Long read L is correctly represented as (u1,r,u2). (Bottom) The region contains highly
similar unipaths r1 and r2 (perhaps differing by only a single indel base). Long read L9 incorrectly passes through r2 rather than r1, perhaps because it has an
sequence. (F) Consensus long reads from across the genome are now used to create a unipath graph using K = 640, about half the long read length. Still
repeats longer than this K cause the genome to be ‘glued’ together. (G) Unipath scaffolding (main text Step III.2). Jumping pairs are now used to connect
unipaths, e.g., u1–u2 and v1–v2 (top), but links to repeats, e.g., u1 to r (bottom) are avoided where possible. (H) Closure (main text Step III.3). (Top) Circular
genome whose assembly might be resolved except for a ‘bubble’ in a repeat region (perhaps with branches differing only by a single base). (Bottom)
Representation of genome in which vertices represent unambiguous sequence (in this case, nearly all of the genome), and edges represent ambiguous
sequences (in this case, two sequences in each of two cases). These edges would correspond to the short unresolved part of the repeat.
Diagram of assembly method. (A) The ideal unipath graph depends on the genome and a constant K, the ‘minimum overlap.’ Perfect repeat
Finished bacterial genomes from shotgun sequence
be obtained by the same method from a less perfect collection of
sequences. In all cases, the method is as described as in Butler at al.
(2008). Here we use K = 96, which is approximately half the length
of the fragments for data type A (the exact value is not significant).
The steps are as follows:
1. As previously described (Gnerre et al. 2011), data type A (read
into single ‘super-reads.’ These are then formed into an initial
unipath graph. This graph is expected to be highly accurate;
however, it has gaps arising from bias in the Illumina data.
2. Because data type C (jumping pairs) can be less biased than
data type A (Supplemental Fig. 1), we next fill some gaps in the
unipath graph using the jumping reads, ignoring their pairing.
These differences in bias are not well understood but might be
attributable to protocol differences between data types or
sample-to-sample variability in protocol instantiation.
3. Next, we use data type B (Pacific Biosciences reads) to fill in
gaps in the unipath graph. This process involves defining data
(r,u1,u2) consisting of part of a long read r that bridges a gap
between unipaths u1and u2, then forming the consensus of the
read parts associated with a given pair (u1,u2), then improving
are inserted into the unipath graph.
Step II: Build unipaths using a minimum overlap of K = 640
By using a larger K, we now build a unipath graph in which only
longer repeats are glued together. Here K = 640 is about half the
read length for data type B (Pacific Biosciences reads).
1. These reads are laid out on the unipath graph, each read being
converted into a sequence u1,...,unof unipaths (or in short, u).
The typical read lands within a single large unipath, providing
essentially no information. However, some reads bridge repeat
boundaries, thus being expressed as a sequence of more than
one unipath (n > 1). These reads provide information; however,
the larger n is, the more likely u is to contain an error. For ex-
ample, in cases in which two unipaths are identical except for
a single-base indel, there is some chance that the Pacific Bio-
sciences read will have an error at the same position, and thus
a chance that the wrong unipath will be placed in u. Thus, at
this stage, we are limited by the resolving power of single reads.
2. Now we form the ‘consensus’ of the sequences u (see Methods).
Here the difficulty is that to find the consensus, we must group
together similar sequences; however, when we do so, it is in-
evitable that different repeat copies will appear in the same
Because differences between repeat copies are difficult to distin-
guish from errors, we do not know a priori how many different
genomic sequences appear in the group, and hence we do not
know how many consensus sequences should be formed.
3. These consensus sequences are used to create the K = 640 uni-
Step III: Build the assembly
1. We use the unipath graph first to determine the fragment size
distribution for data type C (jumping pairs), then estimate the
distances between unipaths. We found that because of the wide
distribution of the jumping pair fragment sizes (2–10 kb), it was
necessary to devise a new statistical model to compute these
2. Now we use the jumping links to connect the unipaths into
a graph. In doing this, we try not to link directly to repeats, but
the biology of our samples (for example, chromosomes and
uniqueness directly using an absolute measure of read density.
3. Each link is then replaced by all possible sequence paths
through the large K unipath graph that are consistent with the
linking information. The totality of the data is then used to
eliminate as many as possible of these ‘alternatives.’
4. This process yields graph assemblies (Fig. 2).
The assemblies generated by this method can contain local
ambiguities, i.e., loci where two or more alternatives are possible,
insofar as the assembly algorithm has been able to determine. We
note that such ambiguities could be due to systematic sequencing
errors, or repeat copies that could not be distinguished, or actual
mixed sites in the input DNA sample. For prokaryotes, these can
arise as mutations in the growing culture. Of course, for eukaryotic
genomes, allelic polymorphism would also give rise to local am-
biguities. Assemblies can also contain global ambiguities, repre-
senting large-scale features that are not fully resolved in the
assembly (Fig. 2).
The graph assemblies that we display here (Figs. 2, 3; Sup-
plemental Fig. 3) have the following semantics. Vertices represent
completely known sequences. Edges between two vertices repre-
and are labeled accordingly. Usually n $ 2, because otherwise the
edge would have been absorbed into one of the vertices, but the
case n = 1 can occur where there is branching in the graph (cor-
responding to global ambiguity), and the case n = 0 corresponds to
To make these graph assemblies accessible to existing pipe-
lines, we convert them into standard FASTA assembly files by se-
representing the actual content of these assemblies and those
produced by other groups (DB Jaffe, I MacCallum, DS Rokhsar, and
MC Schatz, in prep.).
LG and is automatically invoked if long-read data are provided as
input to the algorithm.
We chose 16 bacterial samples to apply our new method to (Table
2). Reference sequences for three of these samples—Escherichia coli
and Rhodobacter sphaeroides—were available, allowing us to use
the remaining samples were selected on the basis of availability,
with the exception of a single sample that was excluded after data
of GC content, from 27% to 69%, thus providing a test of perfor-
mance at GC extremes.
For each sample, we generated data in accordance with the
recipe of Table 1 (for protocols, see Supplemental Methods). In
most cases, the Illumina data sets were generated by pooling 24
libraries within a single lane. Delivered coverage levels varied
depending on production conditions, and we deliberately lowered
Ribeiro et al.
coverage in some cases to get closer to the Table 1 specifications
(Supplemental Tables 2–4), using an initial genome size estimate,
prior to assembly. Note also that coverage levels are difficult to
interpret. For example, for R. sphaeroides, we had nominal long
read coverage in Pacific Biosciences data of 2063, but coverage by
reads $2 kb was only 1.63, whereas for E. coli, nominal read cov-
erage was 643, but coverage by reads $2 kb was 10.63 (Supple-
variability in production conditions, which is unsurprising given
how recently the technology was introduced.
available to compare to; however, in each case, we observed dis-
the quality of both our assemblies and the reference sequences
rigorously, it was necessary to resolve all of these discrepancies. In
previous work (MacCallum et al. 2009), we have described and
validated reference sequence corrections for samples #1–#2: E. coli,
six corrections, and R. sphaeroides, 374 corrections. We note that
some of these corrections involved multiple bases, and in some
cases, large-scale rearrangements of the reference sequences were
corrected. In this study, we make additional corrections: one for E.
coli, and 32 for R. sphaeroides.
For sample #3, S. pneumoniae, we had access not only to our
data from our sample, but also to the primary sequence read data
from which the finished reference was generated, enabling a
comprehensive analysis of the discrepancies between the original
reference sequence and our new read data, which could also ac-
count for true sequence differences between the two samples
themselves. We describe here in detail the nature of the discrep-
ancies, validation methods, and results. First, we note that dis-
crepancies could be due to (1) errors in our data or analysis, or (2)
errors in the original reference sequences, or (3) true biological
differences between the sample used to create the reference se-
quence and our sample for this work. While we could not resolve
this completely without access to the original DNA sample and
extensive laboratory experiments, as we explain below, we were
nonetheless able to estimate the error rate in the original reference
We observed 63 discrepancies between the S. pneumoniae
referencesequenceandour data.An initialinvestigationsuggested
from the original reference. The other three cases were likely sites
that are mixed in the population, for which either of two alter-
natives could be chosen as ‘correct’ (see Supplemental Table 7). We
note that three of the discrepancies (including two of the mixed
sites) occur within a complex 13-kb repeat region, whose exact
we are thus limited in our ability to draw conclusions about the
accuracy of assemblies of this region. We next edited the reference
to introduce these ‘corrections,’ yielding a corrected reference se-
quence. Next, we aligned all of our Illumina reads to both the
corrected reference and the original reference, and counted those
reads that supported one reference but not the other (Supple-
mental Table 7). These counts were overwhelmingly supportive of
the corrections, with support typically in the range of 100 to 1 for
‘corrections’ were bona fide differences between our sample and
the original reference sequence.
We next obtained the 26,174 original Sanger-chemistry reads
fortheS. pneumoniaeproject.We alignedthesereadstotheoriginal
examining the Sanger chemistry traces, producing a report in each
case (summary in Supplemental Table 7; Supplemental Fig. 2). In
summary, we found that 36 of the 63 discrepancies appeared
clearly supported by the data as errors in the reference sequence,
samples. The status of the remaining 11 discrepancies could not be
ascertained from the available sequence read evidence.
edge labeled n represents n possibilities for the sequence lying between its vertex sequences. For n > 1, these are local ambiguities. (1) E. coli. The
assembly represents a circular chromosome that is completely determined except for a single local ambiguity for which there are two alternatives, as
denoted by the edge labeled 2. This ambiguity represents either a T or a G. (2) R. sphaeroides. Each component of the graph is circular and
corresponds to either a chromosome or plasmid, except for plasmids 4 and 5, which are highly similar and joined together in the assembly, resulting
in two global ambiguities. The nine edges with labels exceeding 1 represent local ambiguities. (3) S. pneumoniae. The assembly is a circle. There are
six local ambiguities.
ALLPATHS-LG assemblies of three finished genomes. Vertices in the graph represent completely determined sequences, whereas an
Finished bacterial genomes from shotgun sequence
Finally, we carried out additional laboratory work for 55 of
the discrepancies to determine the exact sequence present in our
all cases, we found that the new Sanger reads support our changes.
In summary, we note that while it is impossible to know the
exact number of error events in each of the reference sequences for
samples #1–#3, we know that for:
E. coli, the number of error events likely is at most seven, and
possibly less, since such a small number of discrepancies could
be attributable to sample mutations;
S. pneumoniae, the number of error events is probably between 36
R. sphaeroides, the number of error events is probably close to 400,
because it seems very unlikely that such a large number of dis-
crepancies could be attributable to differences in DNA sequence
between the samples.
We next applied the assembly algorithm to all 16 data sets
(ALLPATHS-LG revision 41343; computational performance
shownin Supplemental Table 8),usingdefaultparametersineach
case, then assessed the assemblies (Table 3). For the control as-
semblies#1–#3,we could use the correctedreferencesequencesto
assay accuracy precisely.
We first describe the three control assemblies (Fig. 2; Table 3).
For E. coli, there is a single circular contig, which is completely
determined except for a single base. Thus, the entry in Table 3
shows one local ambiguity. There are two errors, both sub-
stitutions, separated by three bases.
For R. sphaeroides, which has two chromosomes and five plasmids,
there are 11 contigs. The extra four contigs are accounted for by
the fact that two of the plasmids share an essentially perfect
19-kb repeat and are consequently glued together in the as-
sembly, forming a ‘twinned’ plasmid structure (Fig. 2). All other
chromosomes and plasmids are present as simple circles. There
are nine local ambiguities, involving 2, 2, 3, 5, 6, 14, 15, 17, and
21 alternatives, respectively, representing uncertainty about the
exact sequence of short regions of size up to ;100 bases, and
occurring mostly in repeat regions. Relatively large numbers of
alternatives (e.g., 21) typically arise where several bases are am-
biguous, resulting in an exponential growth of alternatives. There
are four errors, consisting of three substitutions and one single-
base deletion (G16! G15).
For S. pneumoniae, there is a single circular contig. There are six
local ambiguities. There are no errors.
Critically, we note that (1) in all three cases, there are no gaps;
(2) the contigs for these projects are essentially complete chromo-
somes (or plasmids); and (3) the overall accuracy is substantially
In particular, we note that there were only four incorrect bases for
our assembly of R. sphaeroides, as compared with several hundred
error events for the reference sequence (many involving multiple
bases), and none for our assembly of S. pneumoniae, as compared
with more than 30 for the reference.
We note that the overall contiguity of the 16 assemblies is
very high:the median N50contig size is 2.2 Mb (Table3). Although
we cannot assess the accuracy of the 13 ‘unknown’ genomes, we
assembly algorithm was applied identically in both cases; however, for B, jump coverage was increased by 2.5-fold.
Increased jump coverage simplifies assembly of Eubacterium. Two assemblies (A) and (B) of sample #10 (Eubacterium sp.) are shown. The
Ribeiro et al.
can describe their global properties (Supplemental Fig. 3). For ex-
ample, three of the assemblies (#7, #9, #16) are again simple circles.
Some of the assemblies are completely resolved except for large-
scale global features. For example, #10 (Eubacterium sp.) is a circle
having a single global ambiguity, consisting of two parallel
that are not bridged by the data. In contrast, as suggested by the
number of contigs, scaffolds, and global
ambiguities, some assemblies are less well
resolved. To understand why this might be
the case, we computed the expected num-
ber of jumping pairs that would bridge
windows of specified size (Supplemental
Table 4a). For example, for 2-kb windows,
among samples, this number varies from
28 to 285 (factor of 10), whereas for 6-kb
windows, the number varies from 0.2 to
15 (factor of 75). These data suggest that
for particular samples, the presence of
somewhat longer repeats and/or some-
what less successful jumping libraries
could easily result in failure to bridge all
repeats, and thus a less well-resolved
To a certain extent, less successful
jumping libraries can be compensated for
by increasing coverage. Thus, as an ex-
periment, we enlarged the jump data set
for sample #10 by 2.5-fold by using the
full amount of data that had been gener-
ated, resulting in a striking simplification
of the assembly graph (Fig. 3). Indeed,
because library construction rather than Illumina sequencing per
se is the primary driver of assembly cost for our model, increasing
it is limited in its effect, because intrinsic variation in jumping li-
brary ‘bridging capacity’exceeds10-foldbetweensamples,andthe
capability of a given library to bridge repeats of a given size de-
creases roughly exponentially, by n-fold for each kilobase increase
c(Mb) Ambiguities Accuracyf
# Name Contigs ScaffoldsContig ScaffoldLocald
Error eventsBase quality
F. nucleatum F0419
F. nucleatum 7_1
N. gonorrhoeae FA19
N. gonorrhoeae MS11
aCount is the number of contigs and scaffolds in each assembly.
bGenome size (Mb) is from Table 2.
cN50is the contig (or scaffold) size such that half the assembly bases were included in contigs (or scaffolds) of that size or larger. Gaps were not included in
dLocal ambiguities: Each is an instance where one or more alternatives are reported.
eGlobal ambiguities: These represent unresolved global topology, not representable by a single number; as a proxy, we report the number of vertices in
the graph having multiple entering edges. See Figure 2 for an example.
fAccuracy: Error events are the total number of discrepancies between assembly and corrected reference; base quality is the phred base quality score
(Ewing and Green 1998; Ewing et al. 1998), computed as ?10 3 log10(n/g), where n is the total number of substitution and indel bases occurring in the
discrepancies, and g is the total number of bases in contigs.
gFor sample #3, n = 0 (there are no errors), and thus ?10 3 log10(0) = ‘, but this is not meaningful as a base quality.
Species and strain for each sample.
aGenome size: for 1–3, reference sequence size; for 4–16: assembly size, including gaps.
bGC (%): for 1–3, computed from reference sequence; for 4–16: estimated from assembly.
cReference sequence: finished for 1–3, none available for other samples.
Origin of samples: see Supplemental Table 1. Samples 4–7, 10–13, and 16 were sequenced as part
of the Human Microbiome Project (HMP); see http://www.hmpdacc.org.
Finished bacterial genomes from shotgun sequence
in the repeat size (Supplemental Table 4a), where n ranges from ;2
to 4, depending on library quality.
Perfection of bacterial genome assembly is an important goal since
imperfections, like missing genes, misassemblies, or miscalled ba-
ses may result in incorrect biological conclusions being made re-
garding the biology and evolutionary history of the sequenced
organism (Fraser et al. 2002; Klassen and Currie 2012). In the early
days of sequencing bacterial genomes, great energy and resources
were expended to finish bacterial genomes into their full circular
forms, which wasacceptable because the pace of sequencing itself
was slow. As newer and faster methodologies and sequencing
technologies arrived, perfection was increasingly sacrificed for
speed and cost. Draft genome assemblies can now be rapidly
produced, but they are far from perfect. In this study, we present
assembly methodology. The resulting assemblies appear at least
in some cases to be better than the finished genome reference
sequences produced in the past and yet can be produced rapidly
at a cost that is about an order of magnitude lower (see ‘‘Supple-
Our method starts with three data types, whose accuracy,
evenness of coverage, and range of repeat resolution span a wide
range and are compensatory, thus enabling the results presented
here. We consider the natural question of whether fewer ingre-
dients could be used. First, it is plausible that a substantially
modified algorithm could omit data type A (fragment read pairs),
because jumping reads might provide high-quality coverage in
their place. Second, omission of data type B (long reads) cuts at the
heart of the method and would be expected to have deleterious
N50contig size is >10-fold smaller without these data (Supple-
mental Table 9). Finally, direct measurement of bridging power
generated here have substantially less power than jumping pairs
for linking over distance; however, this could change with improve-
ments to technology.
We note that, beyond generating longer long reads, improve-
ments to laboratory technology could improve results. For exam-
ple, amplification bias might be further reduced (Aird et al. 2011).
This would have significance for medically important pathogens
at GC extremes such as Mycobacterium tuberculosis (high GC) and
Plasmodium falciparum (low GC). Similarly, we have seen signifi-
cant variability in the ability of jumping libraries to bridge long
repeats (Supplemental Table 3a). This variability may be rooted in
DNA extraction protocols or the jumping library protocol itself,
both of which might be improved. Moreover, we note that the
methods described here are designed for DNA from culturable
bacterial strains, and that their extension to amplified material
from single cells could prove challenging.
We have demonstrated a computational method that is fully
automated and pushbutton, using default arguments for all sam-
ples. Our method achieves exceptionally high accuracy, and we
note that this is achieved by explicitly encoding ambiguities that
represent uncertainty regarding the true sequence of the genome.
It would be valuable to classify such ambiguities, for example, to
distinguish between positions that are mixed in the sample and
those that are uncertain because of limitations in the resolving
power of the data. Our methods have been demonstrated only on
bacterial genomes because changes to the algorithm would be
needed to assemble significantly larger genomes. This would be
eased by any future reductions in the error rate of the long read
data. We note that at present, cost considerations might preclude
generation of data by our recipe for large genomes. With changes
to algorithms, coverage requirements might be reduced; however,
we have not carefully controlled for coverage in this study because
With thisworkwemakeclearthatit isnowpossibletorapidly
generate bacterial genome assemblies that are nearly perfect, at
relatively low cost. Importantly, using our approach, these high-
quality genome assemblies could be generated by any researcher
with access to sequence data and computational infrastructure.
This capability will be critical for interpreting genomics-based
studies of bacteria such as those being applied to studies of bacte-
rial epidemiology, which require precise information to track the
emergence and spread of virulence and antibacterial resistance
among bacterial populations infecting humans (Harris et al. 2010;
Lieberman et al. 2011; Parkhill and Wren 2011; Rasko al. 2011b;
to perfection remains important for the field.
For Illumina sequencing, 180-bp insert fragment and ;3-kb jump-
ing whole genome shotgun libraries were generated and sequenced
with 101-base paired-end reads on an Illumina HiSeq 2000 instru-
ment using standard methods (for more details, see Supplemental
Methods). Jumping libraries were size-selected using magnetic
beads rather than agarose gel, thus yielding a wide size distribution.
For Pacific Biosciences sequencing, ;3 kb (plus 6 kb and 10 kb for
samples #4 and #8) insert whole genome shotgun libraries were
generated and sequenced on a Pacific Biosciences RS instrument
using standard methods (for more details, see Supplemental
The algorithm is as described above, with further details provided
here and in Supplemental Methods. In particular, after converting
each long read into a sequence of unipaths, we then form the
‘consensus’ of these sequences (algorithm Step II.2 above, and
Supplemental Methods). In brief, starting from these sequences,
we carry out a local voting process that involves choosing between
two parallel branches in a bubble. This yields a collection of se-
quencess (each itself a sequenceof unipaths).From these, we form
two sets of sequences of unipaths that we call their ‘consensus.’
One consists of one-sided left and right neighborhoods of each
drawn from subsequences of the sequences s. The second consists of
sequencesconstructedfrom s and bridging between two unipaths of
size $1000 k-mers, but otherwise unbounded in length.
The raw data are available via NCBI GenBank (http://www.ncbi.nlm.
nih.gov/genbank). Accession numbers are listed in Supplemental
Tables 5 and 6. The three modified reference sequences and 16 as-
semblies are accessioned in GenBank by the following identifiers,
AKVX = assembly), #2 (AKVW = reference; AKBU = assembly), #3
Ribeiro et al.
2276 Genome Research
(AKVY = reference; AKBW = assembly), #4 (AKBX), #5 (AKBY), #6 Download full-text
(AKBZ), #7 (AKCA), #8 (AKCB), #9 (AKCC), #10 (AKCD), #11
(AKCE), #12 (AKBT), #13 (AKCF), #14 (AKCG), #15 (AKCH), and
on the Broad Institute website at ftp://ftp.broadinstitute.org/pub/
We thank Emma Allen-Vercoe, Laurie Comstock, James Fox,
Glenn R. Gibson, Jacques Izard, Janet Manson, H. Steven Seifert,
Christopher Sibley, Nancy Taylor, Claudette Thompson, Marin
Vulic, and Louise Williams for access to DNA samples. We thank
the Broad Institute Sequencing Platform for generating the data
for this work. We thank Kathryn Keho and the team at Pacific
Biosciences for their support. We thank Nick Patterson for pro-
posing the statistical model that we used to calculate separations
using jumping pairs. We thank Ashlee Earl for help with sample
acquisition, and helpful comments on the manuscript. We thank
Andi Gnirke, Michael Ross, and Mike Zody for valuable discus-
sions about the work. This project has been funded in part with
Federal funds from the National Human Genome Research In-
stitute, National Institutes of Health, Department of Health and
Human Services, under grants R01HG003474 and U54HG003067;
and in part with Federal funds from the National Institute of Al-
lergy and Infectious Diseases, National Institutes of Health, De-
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Received April 9, 2012; accepted in revised form June 13, 2012.
Finished bacterial genomes from shotgun sequence