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Creating new databases

John Nash
2013-10-04
2014-10-08
  • John Nash

    John Nash - 2013-10-04

    I'm a bit unclear on how to create new databases... e.g. I would like to add all Salmonella genomes to the database. Would you be able to write a "how to" in this regard?

    Thanks
    John

     
  • brant

    brant - 2013-10-18

    HI there pathoscope crew,

    great work on the program and congrats on your GR manuscript!

    +1 on the comment above. I'm going to post a ticket for the same request. I understand how i can prepare a SAM file as the database (although some additional clarity on bowtie2 parameters will be helpful), but I'm less clear on the bl8 formatted database... the text of the manuscript suggests the version of BLASTN used is modified and incorporates the GNUMAP algo. is this just the GNUMAP executable from (http://dna.cs.byu.edu/gnumap/running.shtml)?

    thanks much for pathscope,
    b

     
  • brant

    brant - 2013-10-18

    btw, looks like "public" ticket creation is turned off for this project.

     
  • Stephen

    Stephen - 2014-10-08

    +1 to this, and more documentation. Also, would it be possible to use sqlite instead of MySQL?

     

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