2015 Second International Conference on Advances in Computing and Communication Engineering
Efficient Read Alignment Using Burrows Wheeler Transform and Wavelet Tree
Sanjeev Kumar Suneeta Agarwal
Department of CSE Department of CSE
MNNIT, Allahabad MNNIT, Allahabad
U.P., India U.P., India
skgcp86@gmail.com suneeta@mnnit.ac.in
Abstract—In genome sequence alignment problem, a
reference string and number of query strings referred as short
reads, are given, goal is to seek out occurrences of these query
strings in the reference string. Huge amount of reads generated
by new sequencing technologies (Illumina/Solexa) need the
development of an efficient algorithm requiring both less
memory and computational time. There are number of indexing
and string matching techniques to align short reads on reference
string(genome). Size of index of the reference string in each of
existing techniques is large. In this paper, a new self compressed
index technique (BWT-WT) is proposed. BWT-WT scheme is
based on Burrow Wheeler Transform (BWT) and Wavelet tree
(WT). BWT-WT also supports exact alignment of DNA sequence
reads. Performances of BWT-WT with other BWT based tools of
short read alignments are compared. Experiments show that
BWT-WT based program achieves more compression and also
faster searching in comparison to other existing tools.
Keywords—Burrows-Wheeler Transform, FM Index, Full Text
Index, Wavelet Tree and Sequence Analysis.
I. INTRODUCTION
Next generation sequencing machine Illumina/Solexa
generates millions of short reads DNA sequences in a single
run of the machine. These reads must be mapped to one or
more reference genomes. The orientation of a read relative to
genome in not known. To match these reads, the main problem
is how to align the reads to reference genome accounting for
exact matching with a reasonable amount of time and memory
space? There are number of applications where short read
alignments are used. Example includes: assembling reads into a
genome, aligning reads to one reference genome for analysis of
genomic variation, aligning a micro-biome to a set of reference
genomes for species or functional analysis etc.
Searching biological sequences in genome and protein is
important to understand genetic blue print of living organism.
This resulted in a fast development of new technologies
generating vast amounts of sequence data to be analyzed [7].
For this reason, today the focus changed from data acquisition
to efficient data storage and processing methods. To regain the
original ordering of the reads, often they are aligned to a
reference genome, where the massive number of sequences that
need to be processed requires smooth search scheme and data
structures.
A lot of effort has been made to develop methods that are
both memory efficient and fast. One approach to derive
suitable data structures is the Burrows-Wheeler Transform
(BWT), which can be understood as a rearrangement of
characters in a sequence. Therefore, it has been integrated in
978-1-4799-1734-1/15 $31.00 © 2015 IEEE 133
DOI 10.1109/ICACCE.2015.80
Authorized licensed use limited to: UNIVERSITI TEKNOLOGI MARA. Downloaded on April 05,2022 at 07:43:16 UTC from IEEE Xplore. Restrictions apply.
Rajesh Prasad
Department of Computer Science
Yobe State University, Damaturu
Yobe State, Nigeria
rajesh_ucer@yahoo.com
several bioinformatics tools for read mapping, e.g. SOAP [9],
BWA [5], BWA-SW [13] and Bowtie [11].
Four categories of alignment programs are currently used to
map the short reads sequences. First category is based on
hashing of read sequence such as RMAP (Smith et. al., 2008),
MAQ (Li et al 2008(1)) and ZOOM (Li et. al. 2008(2)). These
programs have flexible memory space but do not support
gapped alignment and multithreading. In second category of
alignment, programs are based on hashing of reference genome
such as SOAP (Li et. al. 2008(3)), and BFAST [14]. Programs
of this category supports multithreading for alignment of reads
but size of reference genome index is very large. Third
category programs are based on merge sorting of reference
genome as well as merge sorting of read sequence such as
Malhis (Malhis et. al. 2009) but these programs are not very
much popular as they do not support pair end mapping. Fourth
category of program is based on Burrows Wheeler Transform
(BWT, 1994) which is efficient in both memory footprint as
well as speed. Some of the software programs of this category
are: BWA [5], Bowtie [11] and SOAP [9].
Programs of fourth category mentioned above are having
relatively small memory footprint, efficient in searching and
support exact matching as well as inexact matching with some
bounded allowed differences. Exact matching by these
programs take few seconds to align the reads but to align the
inexact reads it takes too much time to find all the similar
substrings. In case of DNA profiling multiple reference
genomes are used for analysis and identification of gene
behaviour, the size of index again become an issue, so
reduction of index size is required. As a result, development of
efficient program requiring lesser memory and computation
time is need of today.
BWT [2] based algorithm uses number of external tools
such as move to front encoding (which is used to rearrange the
characters in similar order), run length coding and variable
length coding to compress the reference sequence.
The Wavelet Tree [4] was invented in 2003 by Grossi,
Gupta and Vitter, as a data structure to represent a sequence
and answer some queries on it. It is a milestone in compressed
full text indexing which adapts the compressibility of the data
in many ways excellently. Two key approaches to achieve this
are using specific coding (Entropy Coding) on bitmaps and
modifying the tree shape.
In this paper, a new self compressed indexing supporting
exact alignment of DNA sequence reads is proposed, which is
based on BWT & Wavelet Tree. The advantage of BWT-WT
is, it provide index of optimal size and supports number of
queries such as access, rank & select in constant time.
Performance of BWT-WT for DNA sequence alignment is
compared with other BWT based tools. Experiments show that
BWT-WT based program achieves more compression and
efficient searching in comparison to other techniques.
This paper is organized as follows. Sec. II describes the
related concepts. Section III presents proposed compression
and indexing techniques based on Burrows-Wheeler Transform
and Wavelet tree. Sec. IV presents the experimental setup and
analysis of the results. Finally, Sec V concludes the paper.
II. RELATED CONCEPTS
A. Suffix Tree and Suffix Array
Suffix tree [1] has been used as an important data structure in
string processing. This data structure plays a prominent role in
algorithms but is not as prevalent in actual implementations of
software tools. There are two major reasons for this. The first
reason is the space consumption, as the suffix tree requires
quite large space, though its performance is asymptotically
linear. The second reason is that the suffix tree demonstrates a
poor locality of memory reference. It causes a significant loss
of efficiency in architectures of cached processor.
Suffix array [6] is introduced by Manber & Myers [6] as a
simple, space efficient indexing method alternative to suffix
trees. It is key data structure for solving a number of problems
on data compression and information retrieval for biological
sequence analysis and pattern discovery. It is defined as the
permutation of index numbers giving the starting positions of
suffixes of a given string in alphabetical order. Table I shows
the suffix array for the string “AGCAGT$”.
TABLE I. SUFFIX ARRAY FOR TEXT T=AGCAGT$
Suffixes Ordered Suffixes
I S[i] I S[i] Ssuf
0 AGCAGT$ 0 6 $ addition, it allows to obtain the number of occurrences of a
1 GCAGT$ 1 0 AGCAGT$
2 CAGT$ 2 3 AGT$
3 AGT$ 3 2 CAGT$
4 GT$ 4 1 GCAGT$
5 T$ 5 4 GT$
6 $ 6 5 T$
B. Burrrows Wheeler Transform
DNA sequencing algorithms based on Burrows Wheeler
Transform (BWT) [2] are widely used in genome sequencing
analysis. The main concept of BWT is to sort all rotations of a
given string in lexical order in form of BWM (Burrows
Wheeler Matrix) and then return the last column as a result.
This last column, i.e., the BWT string, can be easily
compressed, because it has many repeated characters together.
BWT also allows fast string matching on compressed text. It is
implemented by the following steps:
1. Derive a conceptual matrix M whose rows are n cyclic
shifts of the text T, n being the length of text.
2. Lexicographically sort the text of resultant matrix
called BWM.
134
Authorized licensed use limited to: UNIVERSITI TEKNOLOGI MARA. Downloaded on April 05,2022 at 07:43:16 UTC from IEEE Xplore. Restrictions apply.
3. Construct the transformed text Tbwt by taking the last
column of BWM.
The transformed text Tbwt in the last column is also denoted
as L (last). In particular, the first Column of BWM F (first), is
obtained by lexicographically sorting the characters of T. Fig. 1
shows the construction of BWT.
Index Cyclic Shifting Index BWT Matrix
0 AGCAGT$ 0 $AGCAGT
1 GCAGT$A After 1 AGCAGT$
2 CAGT$AG
Sorting 2 AGT$AGC
3 AGT$AGC 3 CAGT$AG
4 GCAGT$A
4 GT$AGCA
5 GT$AGCA
5 T$AGCAG
6 $AGCAGT 6 T$AGCAG
Fig. 1. Construction of Burrows Wheeler Transform Matrix for Text
T=AGCAGT$. TBWT=T$CGAAG
C. FM-Index
In 2000, six years after the BWT was appeared, Paolo
Ferragina and Giovanni Manzini[3] published a paper
describing how the BWT, together with some small auxiliary
data structures, can be used as a space-efficient index of
reference string T?. They named it as FM Index. Just as the
Last to First Mapping [3, 8] was the key to understanding how
the BWT is reversible, it is also the key to how it can be used
as an index?
D. Wavelet Tree
A wavelet tree [4] is a binary tree of bit strings to represent a
given text T. For an alphabet Σ and a text of length n, the tree
needs O(log2n) bits of storage and supports the determination
of character at a specified position in O(log|Σ|) time. In
given character up to a specified position in O(log |Σ|) time.
Fig. 2 shows the wavelet tree for AGCAGT$.
E. Existing Technique
There are number of techniques for short read alignment to
reference genome such as MAQ, BWA, Bowtie and SOAP .In
Burrows Wheeler Aligner (BWA) [5], short read alignments
are performed. BWA is based on Burrows Wheeler Transform
BWT and FM Indexes [3]. In BWA alignment, an index based
on BWT and Suffix Array is created. To search efficiently
BWA use FM Index [3, 7] which is based on backward search
method. FM Index uses number of other auxiliary data
structures such as count & occurrence table for performing the
search operation. Count table is use to store the number of
characters involved in the string and number of character
smaller than any character c, occurrence table is use to store
the rank of character. The size of suffix array and occurrence
table is too large, so here only sample values are used to store
and other values are calculating on demand. In order to
perform exact matching, count and locate function are used.
Count function return no of occurrence of pattern P into Text
T, whereas Locate function return the location of pattern P
into text T.
 Fig. 2. Wavelet Tree for text T= AGCAGT$
III. PROPOSED ALIGNMENT TECHNIQUE USING BWT-WT
BWA uses the Burrows wheeler based indexing, which takes
space as the size of reference string (in case of human genome
it is 3 billion long). The main disadvantage of above
techniques is that BWT itself does not offer compression but
only arranges the text in compressible form. For compression,
it uses some other external techniques such as Move to Front
encoding (MTF), Run Length Encoding &Variable Length
prefix coding .It requires lots of computation overhead and
use of CPU peak memory. In order to overcome above
problems, here we introduce a new indexing technique BWT-
WT based on BWT and Wavelet Tree (WT). Wavelet tree
compresses the string itself and can also be used as a
component of other compression tool. It also uses binary
succinct data structures RRR [14] (New library that represent
each character in optimal space and gives very fast
Rank/Select operation) to compress the WT nodes, and answer
rank/select queries in constant time. Another advantage of WT
is that it can be extended by changing its shape (Huffman
shape and its variants) and using some compression booster
algorithm to meet a high level compression. The block
diagram of proposed technique is shown in Fig. 3:
135
Authorized licensed use limited to: UNIVERSITI TEKNOLOGI MARA. Downloaded on April 05,2022 at 07:43:16 UTC from IEEE Xplore. Restrictions apply.
Fig. 3. Block Diagram of Wavelet Tree based Indexing and Searching
Technique
A. Index based on BWT-WT:
A wavelet tree encodes a given text T as a binary tree. The
tree is constructed by defining subtext for each node which is
then encoded by bit strings, generated by comparing elements
of the subtext to a pivot element p. Each character c smaller
than p is represented by a ‘0’, while characters greater or equal
than p encoded by a ‘1’.
Now a bit string defines the strings of the child nodes, where
all characters represented by ‘0 ’ forms the new substring of
the left child and all characters encoded by ‘1’ define the
substring of the right child node. A wavelet tree for the BWT
of “AGCAGCAGACT$” and its index is shown Fig. 4 and
Table II respectively.
B. String Searching in the BWT-WT index
Before searching the pattern P into reference string, the
following operations are required. Given the wavelet tree for
the text T, algorithms given in Fig. 5 are used to perform
searching of a string P in to the text T.
 (3) if c is in the left sub-tree of v then
(4) r ← rank0(Bv(r))
(5) v←leftchild(v)
(6) else
(7) r←rank1(Bv(r))
(8) v←rightchild(v)
(9) return i

WTBWT-select(c, i)
(1) v ← leaf representing c: r ← i
(2) while v is not root do
(3) p←parent (v)
(4) if v is in the left child of p then
(5) r←select0(Bp(r)) //selectc(T, i) - the position of the
ith occurrence of c in text T.
(6) else
(7) r ← select1(Bp(r))
Fig. 4. Wavelet Tree Index Based on BWT (8) v ← p
(9) return r
TABLE II. INDEX FOR STRING T = AGCAGCAGACT$

i Suffix# BWT(T) Sorted Suffixes WTsearchT(c, (st, ed))

1 12 T $ 1. Let c[c] be the total number of characters in T that is
alphabetically less than c
2 9 G ACT$
2. st=c[P[i]]+rank(s-1,P[i])+1
3 7 C AGACT$ 3. et=c[P[i]]+rank(e , P[i])
4 4 C AGCAGACT$ 4. return (st, et)
5 1 $ AGCAAGCAGACT$ Fig. 5. String searching functions used in the BWT-WT index
6 6 G CAGACT$
7 3 G CAGCAGACT$
By the use of above functions (Fig.5), suffix interval of pattern
P is derived .For any given pattern P specified by its suffix
8 10 A CT$ range (st,ed) in Suffix Array (SA), operation WTsearchT(c,
9 8 A GACT$ (st, ed)) returns the suffix range in SA of the string P = cP,
10 5 A GCAGACT$
where c is any character st is the start range of Text (initially
s=1) and ed is the end range of Text T (size of text). Find the
11 2 A GCAGCAGACT$A suffix interval of a pattern P into reference string T
12 11 C T$ recursively. Example 1 explains the algorithm.
Example 1:
For the text T = AGCAGCAGACT$ and TBWT =
Following functions are used for backward searching:
TGCC$GGAAAAC. Let pattern P to be searched in text T is
“GCA” Here i=3 (size of pattern), s=1(initially) e=12(size of
BWT-WT access T(i) the text T)
(1) v ← root; r ← i Step 1: for i=3
(2) while v is not a leaf do c=P[i]=P[3]=A
(3) if access Bv(r) = 0 then // access(i)- access the character st=c[A]+rank(0, A)+1=2
at i in text T et=c[A]+rank(12, A)=5
(4) r ← rank0(Bv(r)) // rankc(T, i) - the number of i.e character A occurs in Suffix interval 2 and 5 in Table II
character c at or before position i in text T Step 2: for i=2
(5) v ← leftchild(v) c=P[i]=P[2]=C
(6) else st=c[C]+rank(1,C)+1=5+0+1=6
(7) r ← rank1(Bv(r)) et=c[C]+rank(5,C)=5+2=7
(8) v ← rightchild(v) i.e character CA occurs in Suffix interval 6 and 7 in Table II
(9) return label of v Step 3: for i=1
c=P[i]=P[1]=G
WTBWT-rank(c, i) st=c[G]+rank(5,G)+1=8+1+1=10
(1) v ← root; r ← i et=c[G]+rank(7,G)=8+3=11 [st, et]=[10, 11]
(2) while v is not a leaf do i.e pattern GCA occur in Suffix interval 10 and 11 in Table II

136

Authorized licensed use limited to: UNIVERSITI TEKNOLOGI MARA. Downloaded on April 05,2022 at 07:43:16 UTC from IEEE Xplore. Restrictions apply.
So indices corresponding to pattern P of suffix interval are
[2,5] from table II, Hence pattern GCA occurs in string
T=AGCAGCAGACT$ at two times and their starting position
are 2nd and 5th in text T.
IV. EXPERIMENTAL SETUP & RESULTS ANALYSIS
The experiments were conducted on a HP Pavilion g series
with a 2.8 GHz four-core Intel@CoreTM i3-860 chip with 4
MB L3 Cache, but no parallelism was used. The machine runs
64-bit Ubuntu 12.04 operating system and has 4 GB internal
memory and one 500 GB Serial ATA Hard Drive (7,200
RPM). Following real-world biological and non-biological
data to test the efficiency and usability of proposed method:
1. The human genome sequences from NCBI.
2. Protein data from the Pizza & Chili Corpus .
3. English texts from the Wikipedia dump .
4. Simulated Data of DNA sequence (Arabidopsis thaliana)
and their short read archives (http://plants.ensembl.org/) is
used to compare CPU time depicted in TABLE V.
.
G++4.7.3 is used to build all the source code for experiments
through the Succinct Data Structure Library (SDSL).
TABLE III shows the space required for index prepared to be
used in BWT-WT. Comparison of index size of proposed
approach BWT-WT with other tools BWA [5], Soap [9] and
Bowtie [11] in TABLE IV and Figure 5.Comparision of CPU
time of proposed scheme with others is shown in TABLE 5.

TABLE III. PROPOSED INDEX (BWT-WT) SPACE ANALYSIS

Sequence Input Size Index size Count Number of Size of Construction Time
(N bytes) (bytes) Array size Suffixes Auxiliary (Sec.)
(bytes) (bytes) data (bytes)
(bytes)
English 32619430 36326025~1.11N 1028 2038716 1876136 39.94
DNA 52428801 33881529~0.65N 1028 3276804 3063596 52.567
Protein 52428801 43720341~0.83 N 1028 3276804 3063444 54.801

TABLE IV. INDEX SIZE COMPARISON OF PROPOSED BWT-WT INDEX WITH OTHERS

File File Size Bowtie BWA SOAP BWT-WT

Genome 50 MB 61.5 MB 62.1 MB 114.5 MB 32.3 MB

E-coli 15.3 MB 16 MB 16 MB 30.7 MB 9.9 MB

TABLE V. CPU TIME COMPARISON OF DIFFERENT ALIGNMENT TECHNIQUES

FOR SIMULATED DATA

Program Read Length single pair end read (bp) CPU Time (s)

Bowtie 36 375
Soap 36 249
BWA 36 289
BWT-WT 36 284

137

Authorized licensed use limited to: UNIVERSITI TEKNOLOGI MARA. Downloaded on April 05,2022 at 07:43:16 UTC from IEEE Xplore. Restrictions apply.
 Index
Size
(MB)
Figure 5 Comparison of index size of proposed scheme with others
V. CONCLUSION
In this paper it is shown that how to extend the BWT based
approach to WT based data structure for compressed indexes.
BWT-WT is a simple and faster scheme for short read
alignment. Experiments show that BWT-WT based program
achieves more compression and also efficient searching speed
in comparisons to BWT based approach. As a future work,
one can consider approximate matches (insert, delete, gaps).
REFERENCES
[1] D. Adjeroh, T. Bell, and A. Mukherjee. The Burrows-Wheeler
Transform: Data Compression, Suffix Arrays, and Pattern Matching.
Springer, 1 edition, 2008.
[2] M. Burrows and D. J. Wheeler. A block-sorting lossless data
compression algorithm. Systems Research, Research R(124): pp.1–24,
1994.
[3] P. Ferragina, G. Manzini, V. M¨akinen, and G. Navarro. Compressed
representations of sequences and full-text indexes. ACM Trans.
Algorithms, 3, 2007.
[4] R. Grossi, A. Gupta, and J. S. Vitter. High-order entropy-compressed
text indexes. In Proceedings of the fourteenth annual ACM-SIAM
symposium on Discrete algorithms, SODA ’03, pp. 841–850,
Philadelphia, PA, USA, 2003. Society for Industrial and Applied
Mathematics.
138
Authorized licensed use limited to: UNIVERSITI TEKNOLOGI MARA. Downloaded on April 05,2022 at 07:43:16 UTC from IEEE Xplore. Restrictions apply.
[5] H. Li and R. Durbin. Fast and accurate short read alignment with
burrows–wheeler transform. Bioinformatics, 25(14): pp. 1754–1760,
2009.
[6] U. Manber and G. Myers. Suffix arrays: a new method for on-line string
searches. In Proceedings of the first annual ACM-SIAM symposium on
Discrete algorithms, SODA ’90, pp. 319–327, Philadelphia, PA, USA,
1990. Society for Industrial and Applied Mathematics.
[7] D.Zhang, Q.Liu Compression and Indexing based on BWT: A
Survey.Web Information System and Application Confrence, 2013.
[8] Schindler, M. (1997, March). A fast block-sorting algorithm for lossless
data compression. In Proceedings of the Conference on Data
Compression (Vol. 469). IEEE Computer Society.
[9] Li, R., Li, Y., Kristiansen, K., & Wang, J. (2008). SOAP: short
oligonucleotide alignment program. Bioinformatics, 24(5), pp. 713-714.
[10] B.Langmead, C.Trapnell, M.Pop, S.Salzberg. 2009. Ultrafast and
memory-efficient alignment of short DNA sequences to the human
genome. Genome Biology 2009,Vol.10,Issue 3,Article R25.
[11] Succinct Data Structure Library: https://github.com/simongog/sdsl-lite
[12] H. Li and R. Durbin. Fast and accurate long read alignment with
burrows–wheeler transform. Bioinformatics, 26(5): pp.589-95, 2010.
[13] R. Raman, V. Raman, and S. Srinivasa Rao. Succinct indexable
dictionaries with applications to encoding k-ary trees and multisets. In
SODA, pp. 233–242, 2002.