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  • Plotting length distribution of contigs?

    Hi all,

    I have a fasta file with contigs and I would like to plot the lengths of the sequences. I have only found prinseq-graphs that can do that, but it requires me to install a bunch of perl modules (I believe - I can't find any installation information). Is there an easier way of doing this? Preferably a simple script or java program. Here's an example of some of my data:

    Code:
    >NODE_4_length_492_cov_13.477642
    ACGGAGTATGACTTTGTATTGGTGGGTCCTTGCACTGAACCAGCCCCTCTGGTTGTGCAT
    AGGGGAGGCTTGTGGGAATGTGGAAAGAAATTGGCGTCCTTTACACCTGTTATACAAGAC
    CAGGATCTTGAAGTATTTGTGAGAGAGGTTGGGGACACTTCGTCTGACCTGCTGATTGGG
    GCATTGAGTGATATGATGATAGACAGGCTGGGGTTAAGGGTGCAGTGGTCAGGGGTGGAC
    ATTGTCTCCACACTTAGGGCTGCAGCGCCGAACTGCGAGGGGATCTTGAGTGCGGTTCTT
    GAGGCAGTGGACAACTGGGTGGAGTTCAAAGGTTATGCTCTCTGTTATAGTAAGTCAAAG
    GGGAAGGTGATGGTGCAGTCAAGTGGTGGTAAATTGAGACTGAAGGGCAGAACATGTGAG
    GAGTTGACTAGGAAGGATGAATGCATCGAAGACATTGAGTAGTCTCCTGGCGATGGTTGG
    CTCCCCCGGGGGGGCCCCCGGCGGGGGGTCCCCC
    >NODE_7_length_554_cov_17.906137
    ATTTATTTTGAGTCTTATGTGAAACCACGTGAAGGACCCCAATGTTCTTGTAGTCGCAAC
    AAATGGTCTCACATAAGACTCAAAATAAATCTGCCTCATGAAATTGTCAACAGCATCACT
    AGTGCTCACCACTCTTTCCTCCACTATGGGTTCATGTGTCCTACTGTGAGACAGCCTCAA
    TTCAGATGATAACACAATGTAATGTTCCTCTCTTTTCCATTTCACAATATGTGAGACAAG
    AGATAAGGCTTCACAGTTAACATCCAACGCAACACAGAGATCTAGGAATTTTATTCTAGG
    TGACCACTTCATTTTGGTTGACGCTAGATCACTCATGAATGGCAATATGTGCTTCTCAAA
    CACCGATGGGTACAGCCTTCTCAAAGAATGAATGATGTGATTCAAACCAACCCTATCCTC
    TAATAGTTTTGATGCAGTTGGCTTTAAAGGAAAATAGTCACAAGGGTTATGCTTGAAAAA
    ATCCAATACCTTAACTGTCTTAGGTTCCCCTAAGACCCATGCACCCAACTCTATTGCAGT
    TGATAAGGAGATGCACATATAATCCCATAACAAGGG
    >NODE_8_length_274_cov_16.138685
    CCAAAATAAGTTGTCTTCCACTTTCACTCGAGGTGCGCAGAAATTGCTATCTGAAGCTAT
    CAACAAGTCTGCATTCCAGAGCTCCATTGCATCTGGCTTTGTGGGGTTATGCAGAACATT
    GGGTAGCAAATGTGTTCGGGGACCAAATAAGGAGAATCTGTATATTAAGTCCATTCAGTC
    TCTGATTTCTGATGTCAAGGGAATCAAATTATTGACAAATTCTAATGGCATTCAGTATTG
    GCGGGTTCCGCTAGAACTTAGAGATGGGAGTGGAAGTGAAAGTGTGGTCAGTTATT
    I would like to plot the lengths similar to this:

  • #2
    Using Biopieces you can use plot_distribution like this:

    Code:
    read_fasta -i contigs.fna | plot_distribution -k SEQ_LEN -x
    
    
                                      Distribution
          +          +          +          +           +          +          +
      14 ++*---------+----------+----------+-----------+----------+----------+-++
          |*                                                                   |
      12 ++*                                                                   ++
          |*                                                                   |
          |*                                                                   |
      10 ++*                                                                   ++
          |*                                                                   |
       8 ++*                                                                   ++
          |** *                                                                |
       6 ++****                                                                ++
          |****                                                                |
       4 ++*******                                                             ++
          |*******                                                             |
          |***********       * *                                               |
       2 ++**********************                                              ++
          |******************************************* **  * *            *    *
       0 ++*******************************************-**--*-*----+-------*--+-*+
          +          +          +          +           +          +          +
          0        10000      20000      30000       40000      50000      60000
                                         SEQ_LEN

    It is also possible to output to X11 terminal or PNG, PDF, PS, and SVG.

    Installing Biopieces requires a working setup of Perl w. relevant modules and Ruby w. relevant gems. However, it should be worth the trouble since Biopieces is a nice toolbox IMHO.

    Comment


    • #3
      There's a "Histogram of sequence lengths" example in the Biopython Tutorial, it uses
      Not Java, but also not Perl

      Comment

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