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  • help using velvet for de novo assembly

    Hi everyone, i'm trying to run de novo assembly using velvet on short (100bp long) paired end reads.
    I first ran velveth and it created only two files named: Log and Sequences.
    It also gave me this error:
    velveth: Can't malloc 121 chars: Cannot allocate memory

    I tried to run velvetg but then I got an error:
    [0.000000] No Roadmap file to build upon! Please run velveth (see manual)

    This is what I ran using velveth:
    $ velveth output_assem 35 -shortPaired -fasta file_PE-1.fa file_PE-2.fa

    The two fasta files are already in paired
    What does this mean? This is my first time using velvet, and I will appreciate anyone's help. Thanks a lot in advance

  • #2
    I think velvet wants the fastqs to be interleaved. It least older versions did, and they used to include a little perl script that would do that,

    Comment


    • #3
      Originally posted by swbarnes2 View Post
      I think velvet wants the fastqs to be interleaved. It least older versions did, and they used to include a little perl script that would do that,
      Currrent versions of velvet accept interleaved or separate input files for paired end reads. The default is interleaved; if you are using separate files you have to add the '-separate' option. For your example this would be:
      Code:
      $ velveth output_assem 35 -shortPaired -fasta -separate file_PE-1.fa file_PE-2.fa

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      • #4
        Thanks for the suggestions! I do appreciate them! I am going to try them, hopefully no errors will pop up

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        • #5
          Hii can anyone help me to run velvet with higher hash value rather than 31 and also how to run velvet optimiser? (illumina short paied end reads)
          thanks in advance

          Comment


          • #6
            to use kmer sizes greater than 31, you need to recompile velvet with

            'make ’MAXKMERLENGTH= ’, and put in the max value that you want to be able to use.

            See the velvet manual

            Comment


            • #7
              Hello mastal
              first of all thanks for ur reply.
              i have tried this too but it is showing an error as 'compilation terminated.make: *** [obj/readSet.o] Error 1'

              Comment

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