<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>

CC BY-SA 4.0
2020-12-20T16:23:22.433Z
Hi, YP CHEN, could I know what kind of genome it is? bacterial? viral? eukaryotic? How long is the genome?
juanjo75es
CC BY-SA 4.0
2020-12-21T02:27:00.147Z
Fungal genomes， genome sizes are about ~ 50M
YP CHEN
CC BY-SA 4.0
2020-12-21T06:22:17.267Z
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.
juanjo75es
<genome><assembly>
How to filter a genome assembly consistsing of a large number of contigs?
# 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, YP CHEN, 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.  

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## 0 answers

