Short read alignment
BNFO 601
Short read alignment
• Input:
– Reads: short DNA sequences (upto a few hundred
base pairs (bp)) produced by a sequencing
machine
• Reads are fragments of a longer DNA sequence present
in the sample given as input to the machine
• Usually in the millions
– Genome sequence: a reference DNA sequence
much longer than the read length
Short read alignment
• Applications
– Genome assembly
– RNA splicing studies
– Gene expression studies
– Discovery of new genes
– Discovering of cancer causing mutations
Short read alignment
• Two approaches
– Hashing based algorithms
•
•
•
•
BFAST
SHRIMP
MAQ
STAMPY (statistical alignment)
– Burrows Wheeler transform
• Bowtie
• BWA
BFAST overview
PLoS ONE 4(11): e7767.
BFAST algorithm
PLoS ONE 4(11): e7767.
BFAST masked keys
Short read alignment
Empirical performance:
• Simulated data:
– Extract random substrings of fixed length with
random mutations and gaps
– Realign back to reference genome
• Real data:
– Paired reads: two ends of the same sequence
– Count number of paired reads within 500 to 10000
bases of each other
Short read alignment
Courtesy of Genome Res. June 2011 21: 936-939;
Short read alignment
Courtesy of Genome Res. June 2011 21: 936-939;
Short read alignment