Greetings!
I am doing some de novo genome assembly of a 23Mb genome using Velvet 1.2.10 and quality trimmed MiSeq (Illumina) reads that average about 180bp in length. I have assembled different individuals of this species before with 100bp reads and the kmer size always comes in around 61 for the best N50s and very good max. contig size. However with this assmebly I am getting really low kmer sizes as optimal (for N50s) in the the low/mid 30s. Velvet estimated the kmer coverage averaging 23X.
Results here (Kmer size is on the x-axis, the left y-axis is for the max. contig size ("max," red line) and the left y-axis if for the N50s (blue line)):
I am concerned about how good an assembly would be for such a large genome and such small kmer, and I also just wonder why -- with longer reads -- I need smaller kmers.
Thanks!
I am doing some de novo genome assembly of a 23Mb genome using Velvet 1.2.10 and quality trimmed MiSeq (Illumina) reads that average about 180bp in length. I have assembled different individuals of this species before with 100bp reads and the kmer size always comes in around 61 for the best N50s and very good max. contig size. However with this assmebly I am getting really low kmer sizes as optimal (for N50s) in the the low/mid 30s. Velvet estimated the kmer coverage averaging 23X.
Results here (Kmer size is on the x-axis, the left y-axis is for the max. contig size ("max," red line) and the left y-axis if for the N50s (blue line)):
I am concerned about how good an assembly would be for such a large genome and such small kmer, and I also just wonder why -- with longer reads -- I need smaller kmers.
Thanks!
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