I did some de novo genome assemblies with Illumina PE data using SPAdes, whereas most of them consisting of a large number of contigs(>1000). I have several questions below.

  1. Do we need to filter short contigs?
  2. How to determine the appropriate length threshold?
  • $\begingroup$ Hi, YP CHEN, could I know what kind of genome it is? bacterial? viral? eukaryotic? How long is the genome? $\endgroup$
    – juanjo75es
    Commented Dec 20, 2020 at 16:23
  • $\begingroup$ Fungal genomes, genome sizes are about ~ 50M $\endgroup$
    – YP CHEN
    Commented Dec 21, 2020 at 2:27
  • $\begingroup$ Thanks. I can't help in that case. But I guess what determines your length threshold is what use you intend to make from that assembly. $\endgroup$
    – juanjo75es
    Commented Dec 21, 2020 at 6:22


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