Body: <p>I did some de novo genome assemblies with Illumina PE data using SPAdes, whereas most of them consisting of a large number of contigs(&gt;1000). I have several questions below.</p>
  <ol>
  <li>Do we need to filter short contigs?</li>
  <li>How to determine the appropriate length threshold？</li>
  </ol>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-12-20T16:23:22.433Z
Comments.Text: Hi, YP CHEN, could I know what kind of genome it is? bacterial? viral? eukaryotic? How long is the genome?
Comments.UserDisplayName: juanjo75es
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-12-21T02:27:00.147Z
Comments.Text: Fungal genomes， genome sizes are about ~ 50M
Comments.UserDisplayName: YP CHEN
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-12-21T06:22:17.267Z
Comments.Text: 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.
Comments.UserDisplayName: juanjo75es
Tags: <genome><assembly>
Title: How to filter a genome assembly consistsing of a large number of contigs?
ThreadText: # How to filter a genome assembly consistsing of a large number of contigs?
  
  (Asked by: username_0 on 2020-12-20)
  
  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？
  
  **Tags:** genome, assembly
  
  > **Comments:**
  > **username_1**: Hi, username_0, could I know what kind of genome it is? bacterial? viral? eukaryotic? How long is the genome?  
  > **username_0**: Fungal genomes， genome sizes are about ~ 50M  
  > **username_1**: 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.  
  
  ---
  
  ## 0 answers
  
  