Question: Comparing contigs results from two different assembler
1
gravatar for  '
4.2 years ago by
'260
'260 wrote:

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 • 2.1k views
ADD COMMENTlink modified 3.4 years ago • written 4.2 years ago by '260

Mummer maybe ?

ADD REPLYlink written 4.2 years ago by poisonAlien2.8k

Crossposted: http://seqanswers.com/forums/showthread.php?t=66042

ADD REPLYlink modified 11 weeks ago by RamRS26k • written 4.2 years ago by Daniel Swan13k
1
gravatar for  '
3.4 years ago by
'260
'260 wrote:

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.

ADD COMMENTlink written 3.4 years ago by '260

Great and what is the conclusions?

ADD REPLYlink modified 3.4 years ago • written 3.4 years ago by Medhat8.6k

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

ADD REPLYlink modified 3.4 years ago • written 3.4 years ago by genomax80k
2
gravatar for aleimba
4.2 years ago by
aleimba130
Germany
aleimba130 wrote:

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

ADD COMMENTlink written 4.2 years ago by aleimba130
2
gravatar for h.mon
4.2 years ago by
h.mon29k
Brazil
h.mon29k wrote:

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).

ADD COMMENTlink written 4.2 years ago by h.mon29k
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