1 / 11

Short read alignment

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

avari
Download Presentation

Short read alignment

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript


  1. Short read alignment BNFO 601

  2. 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

  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 molecule • 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

More Related