Comparing contigs results from two different assembler
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5.2 years ago
' ▴ 280

I have done genome assembly on a bacteria sample using SPAdes and Velvet. I have a contigs file from each of the assemblers. How can I compare these two files to see if their results are different or not?

 

Assembly • 2.6k views
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Mummer maybe ?

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4.4 years ago
' ▴ 280

I ended up using progressiveMauve, MUMmer (specifically MUMmerplots), QUAST, and clc_sequence_info (from CLC Genomics Workbench) altogether and I could come to some conclusions based on the results of all these methods.

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Great and what is the conclusions?

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Perhaps the conclusions are only useful to @Lazarus. It appears to have taken 9 months to get to them :)

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5.2 years ago
aleimba ▴ 130

There are several assembly metrics packages out there, if that's what you want. The most popular is QUAST (Quality Assessment Tool for Genome Assemblies):

http://bioinf.spbau.ru/quast

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5.2 years ago
h.mon 32k

Check this thread - it is old, but answers kept being added. In addition to QUAST, see BUSCO (checks for conserved gene content) and something like ALE or REAPR (assembly quality based on mapping metrics).

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