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  • K-mer selection using jellyfish

    Hi

    I am using Jellyfish for the first time. I have used this tool for a set of sample with k-mer lengths 17, 21, 25 and 31. This gave me different genome sizes. Now, how do I establish which k-mer length to select for the estimated genome size as they are varying and not close to the draft genome size. Kindly help. Thanks.

  • #2
    Refer here:

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    • #3
      Estimation of genome size from Nanopore sequence using jellyfish

      Hi,
      I would like to calculate the genome size from the whole genome ONT nanopore reads (~8.7 GB) for a plant genome. My aim is to assemble the mitochondrial genome from ONT nanopore reads. I knew the approximate chloroplast genome size (165kb) and the mitochondrial genome is ~1 MB. But I do not know the depth coverage and expected genome size. I am very beginner and don't know how to calculate both depth coverage and genome size. I have used jellyfish and 27 kmer length to calculate the genome size but not able to get a good result.
      input parameter:
      ./jellyfish count -m 27 -s 100M -t 10 -C ONT.fastq

      Please help me to find out the expected genome size.
      Thank you.

      0 0
      1 7989688383
      2 166231294
      3 43211315
      4 18926377
      5 10427587
      6 6516393
      7 4405895
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      9 2350173
      10 1813597
      11 1432766
      12 1158622
      13 951965
      14 795509
      15 672888
      16 575600
      17 498467
      18 434147
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      118 4604
      119 4561
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      121 4418
      122 4498
      123 4306
      124 4235
      125 4072
      126 3929
      127 3961
      128 3912
      129 3702
      130 3737
      131 3631
      132 3505
      133 3537
      134 3440
      135 3346
      136 3321
      137 3261
      138 3247
      139 3063
      140 3174
      141 3070
      142 3152
      143 2913
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      145 2868
      146 2733
      147 2736
      148 2683
      149 2722
      150 2576
      151 2558
      152 2647
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      166 2097
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      170 1989
      171 2029
      172 1917
      173 1965
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      182 1778
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      196 1621
      197 1598
      198 1526
      199 1583
      200 1564
      Last edited by bioramg; 04-14-2020, 12:00 AM. Reason: Incorporation of additional data

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