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Can SMRT analysis pipeline support fastq files?

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  • Can SMRT analysis pipeline support fastq files?

    Hello,

    I am new to PacBio data and pipeline. Recently, I got some pacBio data in fastq format instead of bas.h5 format. I tried blasr to run alignment and looks like blasr worked. But I want to try HGAP in SMRT analysis pipeline to do de novo assembly. I read a lot of online posts and did not find how to run HGAP with fastq files. Looks like the SMRT pipeline only support bas.h5 as the input files. Does anyone give me some suggestions how to run de novo assembly with HGAP using the fastq files as input?

    Your response would be really appreciated!

    Michael

  • #2
    Originally posted by xuguorong View Post
    Hello,

    I am new to PacBio data and pipeline. Recently, I got some pacBio data in fastq format instead of bas.h5 format. I tried blasr to run alignment and looks like blasr worked. But I want to try HGAP in SMRT analysis pipeline to do de novo assembly. I read a lot of online posts and did not find how to run HGAP with fastq files. Looks like the SMRT pipeline only support bas.h5 as the input files. Does anyone give me some suggestions how to run de novo assembly with HGAP using the fastq files as input?

    Your response would be really appreciated!

    Michael
    Hi Michael,

    You have two options:
    1) Contact your service provider and obtain the original *.bas.h5 files
    2) Use FALCON to assemble your genome from *.fasta files. FALCON is essentially the bleeding edge "command-line" version of HGAP. Depending on your UNIX experience, this may or may not be feasible for you.

    You can download FALCON and it's associated dependencies in one package here:
    https://github.com/PacificBiosciences/FALCON-integrate

    Comment


    • #3
      try to use canu

      Comment


      • #4
        Thank you so much! I will try FALCON!

        Originally posted by gconcepcion View Post
        Hi Michael,

        You have two options:
        1) Contact your service provider and obtain the original *.bas.h5 files
        2) Use FALCON to assemble your genome from *.fasta files. FALCON is essentially the bleeding edge "command-line" version of HGAP. Depending on your UNIX experience, this may or may not be feasible for you.

        You can download FALCON and it's associated dependencies in one package here:
        https://github.com/PacificBiosciences/FALCON-integrate

        Comment


        • #5
          Thank you so much! Canu looks cool and I will try it!

          Originally posted by gconcepcion View Post
          Hi Michael,

          You have two options:
          1) Contact your service provider and obtain the original *.bas.h5 files
          2) Use FALCON to assemble your genome from *.fasta files. FALCON is essentially the bleeding edge "command-line" version of HGAP. Depending on your UNIX experience, this may or may not be feasible for you.

          You can download FALCON and it's associated dependencies in one package here:
          https://github.com/PacificBiosciences/FALCON-integrate
          Originally posted by xthua View Post
          try to use canu

          Comment

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