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  • using bfast for mapping bacterial and viral genomes

    Hi All

    I was intending to map SOLID reads to the viral and bacterial genomes, and was thinking if i can use the same indices as mentioned in the Bfast manual, or do i need to create new ones?

    After reading under advanced topics in the manual, i felt that using the same indices might just be stringent. Can someone throw some more light on this?

  • #2
    Originally posted by kakar_nipun View Post
    Hi All

    I was intending to map SOLID reads to the viral and bacterial genomes, and was thinking if i can use the same indices as mentioned in the Bfast manual, or do i need to create new ones?

    After reading under advanced topics in the manual, i felt that using the same indices might just be stringent. Can someone throw some more light on this?
    They should work well for the viral and bacterial genomes.

    Comment


    • #3
      Originally posted by kakar_nipun View Post
      Hi All

      I was intending to map SOLID reads to the viral and bacterial genomes, and was thinking if i can use the same indices as mentioned in the Bfast manual, or do i need to create new ones?

      After reading under advanced topics in the manual, i felt that using the same indices might just be stringent. Can someone throw some more light on this?
      There has been a lot of work behind the default indexes used for human (check support material from the paper). There is also code butil/btestindexes that
      can help you test how they behave with different error rates, indels, etc... I would strongly suggest to create your own indexes (and compare with the default ones).
      -drd

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