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  • De novo genome assembly question: which assembly should I use?

    I have sequenced two individuals and done three libraries per individual each with a different insert size (170, 500, 800).Using flow citometry I know this genome is 332MB. Also I know is diploid and the genetic variation is not to high. I have done different assemblies for a this plant genome and found this two were the best:

    One Individual
    3 libraries
    Insert size 170, 500, 800
    Number of clean reads 70,287,710
    Number of contigs 134,557
    Mean N50 length (bp) 5,050
    BUSCO 78.54


    Two Individuals
    2 individuals
    6 libraries
    Insert size 170, 500, 800
    Number of clean reads 209,022,970
    Number of contigs 446,608
    Mean N50 length (bp) 4,010.65
    BUSCO 76.38

    I then ran PEP_SCAFFOLDER in this two alignments and got this

    One Individual
    3 libraries


    Main genome scaffold total: 136339
    Main genome scaffold sequence total: 189.946 MB
    Main genome contig N/L50: 17091/2.413 KB

    Two Individuals
    2 individuals
    6 libraries


    Main genome scaffold total: 444336
    Main genome scaffold sequence total: 332.652 MB
    Main genome contig N/L50: 83374/706

    I have two questions:
    1. Would you annotate any of these two genomes?
    2. Which one would you annotate and why?

    Thanks,
    Tatiana

  • #2
    Annotation may reveal what's not there, esp if you know from exp that a given gene is present (eg someone PCR/subcloned ). Guessing eukaryote and that you may have hit some contigs that are repeat heavy (eg contig is pure repeat), and perhaps that your library isn't traversing those repeats?

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