1. CSC2431 February 3rd 2010 Alecia Fowler
Fast and Accurate Short Read Alignment with Burrows-Wheeler Transform Heng Li and Richard Durban
CSC2431
February 3rd 2010
Alecia Fowler

2. Short Read Alignment
SPEED AND ACCURACY

3. Burrows Wheeler Aligner
OVERVIEW: based on backward search and Burrows-Wheeler Transform (BWT)
FEATURES: performs gapped alignment for single-end reads, supports paired-end mapping, generates mapping quality
PLATFORM: Illumina; SOLiD; 454; Sanger
PROS: fast
CONS: short read algorithm is slow for long reads and reads with high error rate

4. Prefix trie
X = GOOGOL$
“G”
“GO”
“GOO”
“GOOG”
“GOOGO”
“GOOGOL”

5. Burrows-Wheeler Transform (BWT)
Algorithm used for data compression
Output is easier to compress as it groups similar symbols together
Text compression method
Takes a block of data and rearranges it using a sorting algorithm
String is built by sorting all of the circular shifts of a string and concatenating the last characters of each circular shift
Key feature is the first-last property, in that the k-th occurrence of a character in the BWT string corresponds to its kth occurrence in the list of sorted circularshifts

6. Suffix array interval and sequence alignment

7. Exact and Inexact Matching
W = LOL
X = GOOGOL$
Has to account for mismatches or gaps in the reads
the BWT index of the reverse reference sequence narrows the search space

8. Evaluation: Simulated Data
Simulated reads from human genome
One million pairs of different lengths
Mapped to the human genome
BWA was found to be more accurate than Bowtie and SOAPv2
Would need to sacrifice mapping quality in order to increase speed

9. Evaluation: Real Data
12.2 million pairs of 51bp reads from a male genome
Mapped to human genome and a human-chicken hybrid reference
Had high speed and accuracy for both