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  • Assembly paired-end sequences with Velvet

    I have sequences from illumina HiSeq 2000. I'll show you the sequence data that I have a bacteria.

    fernando@InvDllo04[Lactobacillus] grep -c "^@" *.fq
    FCHCTVLADXX_L1_wHAIPI016080-93_1.fq:1106031
    FCHCTVLADXX_L1_wHAIPI016080-93_2.fq:1106031
    FCHCTVLADXX_L2_wHAIPI016080-93_1.fq:1088418
    FCHCTVLADXX_L2_wHAIPI016080-93_2.fq:1088418


    As you can see, I have four files with 1106031, 1106031, 1088418, 1088418 sequences. I'm trying to perform an assembly with Velvet. but I am very confused because I do not know how to use these files. I was reading in some blogs and they say it is necessary to use a script from Velvet (shuffleSequences_fastq.pl), i.e.

    1) shuffleSequences_fastq.pl FCHCTVLADXX_L1_wHAIPI016081-94_1.fq FCHCTVLADXX_L1_wHAIPI016081-94_2.fq FCHCTVLADXX_L1_wHAIPI016081-94_shuffled.fq

    2) shuffleSequences_fastq.pl FCHCTVLADXX_L2_wHAIPI016081-94_1.fq FCHCTVLADXX_L2_wHAIPI016081-94_2.fq FCHCTVLADXX_L2_wHAIPI016081-94_shuffled.fq

    3) velveth auto 31,45,2 -fastq -shortPaired1 FCHCTVLADXX_L1_wHAIPI016081-94_shuffled.fq -fastq -shortPaired2 FCHCTVLADXX_L2_wHAIPI016081-94_shuffled.fq

    4) velvetg auto_31 -exp_cov auto

    I do not know if I'm doing the right thing using the shuffled scritp or if I should just use the option "-separate" and run Velvet as follows:

    velveth Assem 31 -shortPaired -fasta -separate left.fa right.fa

    where:
    -separate: Read 2 separate files for paired reads
    -short -shortPaired
    -short2 -shortPaired2

    And the run "velvetg"...

    My confusion here is because I have apparently two files "left.fa" and two "rigth.fa" instead of one as in the previous example.

    I'd like you to tell me how to run Velvet

    Thank you very much.

  • #2
    Don't have experience with velvet, because I found the setup very un-intuitive, and couldn't be bothered with it -> therefore some recommendation to you, use something else then.
    e.g. Ray is easy to setup, and can handle more than one library.

    Comment


    • #3
      If you want to use velvet, I would concatenate your two read1 files together, and concatenate your read2 files together, then run it:

      cat *_1.fq >r1.fq
      cat *_2.fq >r2.fq

      velveth Assem 31 -shortPaired -fastq -separate r1.fq r2.fq
      velvetg Assem

      A value higher than 31 is probably better for kmer length; that's just an example.

      Comment


      • #4
        Next seq data with velvet

        How to run velvet with Next seq data. It has four single reads??

        Thanks
        Bioinform

        Comment


        • #5
          Are you talking about 2 paired NextSeq libraries? Or do you mean Nextera LMP, which ends up (typically) with 4 output files for a single library after you process it?

          Comment

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