How to assess the quality of metagenomics assembly?
2
2
Entering edit mode
9.7 years ago
beloved2012 ▴ 20

Hello everyone! I'm a beginner of metagenomics research. Presently we use soapdenovo package to perform metagenomics assembly then choose the optimal Scaffold according to N50 length (the longest one). I'm wondering that how should we assess the quality of metagenomics assembly except according to the N50 length? Thanks very much!

Assembly Metagenomics • 4.8k views
ADD COMMENT
0
Entering edit mode

OK, thanks all of you. I'll try QUAST later.

ADD REPLY
2
Entering edit mode
9.7 years ago

Quast is, indeed, very useful. However, it is most useful when you have a reference, where it can calculate the number of misassemblies and error rates. For metagenomes, another crucial metric - arguably, the most important metric - is the percentage of reads that map back to the assembly. If only 50% of your reads map to the assembly... it is not very complete. But if 95% of your reads map to the assembly, then even if it is somewhat fragmented, that's probably very good.

ADD COMMENT
0
Entering edit mode

It might also help to look at the percentage properly paired reads to detect any chimeras, something that seems especially relevant in a metagenome assembly.

ADD REPLY
1
Entering edit mode
9.7 years ago

Try quast

It gives you a report with the quality of your assembly.

ADD COMMENT

Login before adding your answer.

Traffic: 1198 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6