Header Leaderboard Ad


Running kmergenie



No announcement yet.
  • Filter
  • Time
  • Show
Clear All
new posts

  • Running kmergenie

    Hello every one.
    I'm new on bioinformatics. So, sorry if my question is too basic.
    I'm trying to run kmergenie. It hasn't worked when I use reads_file.txt with the files I want to calculate the best k-mer. That's what I'm trying:
    $ nano reads_file.txt
    -> Paste:


    $ kmergenie -l 21 -k 51 -s 5 reads_file.txt -o 47G_kmergenie

    The message is:
    running histogram estimation
    File reads_file.txt starts with character ".", hence is interpreted as a list of file names
    Reading 2 read files

    End then it stops.
    The only way kmergenie has worked is running one file at the time, but as I have paired end reads it's gonna take too long to finish the work.
    Please can anybody help me?

  • #2
    I think the file with the path for your FASTQs go after `kmergenie `

    Here is the program syntax: kmergenie <read_file> [options]

    I wrote this tutorial on how to use it - https://onestopdataanalysis.com/esti...-for-assembly/
    Last edited by one_stop; 03-07-2020, 09:58 PM.
    Data Scientist and blogger (http://onestopdataanalysis.com)


    • #3
      The computer analysis of APOL1 and single nucleotide polymorphisms in chronic kidney disease (CDK). Any help anyone can provide me with will be really appreciated. Thank you very much, everyone


      • #4
        KmerGenie estimates the high-quality k-mer period for genome de novo assembly." More info are at KmerGenie


        Latest Articles


        • seqadmin
          A Brief Overview and Common Challenges in Single-cell Sequencing Analysis
          by seqadmin

          ​​​​​​The introduction of single-cell sequencing has advanced the ability to study cell-to-cell heterogeneity. Its use has improved our understanding of somatic mutations1, cell lineages2, cellular diversity and regulation3, and development in multicellular organisms4. Single-cell sequencing encompasses hundreds of techniques with different approaches to studying the genomes, transcriptomes, epigenomes, and other omics of individual cells. The analysis of single-cell sequencing data i...

          01-24-2023, 01:19 PM
        • seqadmin
          Introduction to Single-Cell Sequencing
          by seqadmin
          Single-cell sequencing is a technique used to investigate the genome, transcriptome, epigenome, and other omics of individual cells using high-throughput sequencing. This technology has provided many scientific breakthroughs and continues to be applied across many fields, including microbiology, oncology, immunology, neurobiology, precision medicine, and stem cell research.

          The advancement of single-cell sequencing began in 2009 when Tang et al. investigated the single-cell transcriptomes
          01-09-2023, 03:10 PM