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Which PacBio ouputs use to do novo assembly?



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  • Which PacBio ouputs use to do novo assembly?

    Hello, I was given all the outputs of the result of a whole genome sequencing of a bacteria, and there is a lot of them and I don’t understand which one of these I should use to do a novo assembly:
    • 3 *.subreads.fastq
    • 3 *.subreads.fasta
    • 3 *.bax.h5
    • 1 *.bas.h5
    • 1 *.mcd.h5
    • 1 *.metadata.xml

    I was thinking using SMRT link to do the analysis , but I don’t know which one of these I should use.

    Thanks in advance.

  • #2
    If you are planning to use SMRTlink then use the bax and bas files.

    There are other options like flye (https://github.com/fenderglass/Flye ) and canu (https://github.com/marbl/canu) that may be better than SMRTlink and they can use the fastq files.


    • #3
      Thank you for your answer

      I allready try canu but for somme resons it dosn't get installed...
      I will try to have a look at flye

      But for SMRT link I don't understand to what the bas and bax files correspond to (see image)


      • #4
        Import your metadata.xml file as "RSII Metadata (XML)" data type.


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