Short read alignment
BNFO 601
Short read alignment
• Input:– Reads: short DNA sequences usually up to 100
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 number 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 algorithmPLoS 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 molecule– 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