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Short read alignment

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

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Short read alignment

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  1. Short read alignment BNFO 601

  2. 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

  3. Short read alignment • Applications • Genome assembly • RNA splicing studies • Gene expression studies • Discovery of new genes • Discovering of cancer causing mutations

  4. Short read alignment • Two approaches • Hashing based algorithms • BFAST • SHRIMP • MAQ • STAMPY (statistical alignment) • Burrows Wheeler transform • Bowtie • BWA

  5. BFAST overview PLoS ONE 4(11): e7767.

  6. BFAST algorithm PLoS ONE 4(11): e7767.

  7. BFAST masked keys

  8. 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

  9. Short read alignment Courtesy of Genome Res. June 2011 21: 936-939;

  10. Short read alignment Courtesy of Genome Res. June 2011 21: 936-939;

  11. Short read alignment

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