Comparing and merging genome assemblies

megh · 08-04-2011, 09:25 PM

Hi,

We have recently completed the de-novo assembly of a eukaryotic genome. The genome size is ~3.1GB.
We used two different assembly platforms/pipelines and got ~2.0GB and ~2.8GB scaffolds respectively.

I look for your suggestions in the following areas:

1) What would be the most suitable way to compare the similarity and/or differences between two assemblies?

2) Any suitable assembly merger? The objective of question (1) is to merge them to make it larger.
[ I could not install GAM (Genome Assembly Merger) on my MAC OSX 10.6 ]

3) Any suitable and open-source pipeline for annotation?

Regards.

colindaven · 08-05-2011, 02:31 AM

1) Blast is nice, visualised with Circos. Perhaps try circoletto ?

2) Apparently SSPACE is quite good, haven't tried it yet myself.

sphil · 08-05-2011, 04:21 AM

Actually there are some genome aligners. They differ in speed, amount of genomes which can be aligned and spped. For a first sigh you can use:

Whole genome aligner:
MUMer
LAGAN
AVID (not open source)

or Multi Genome aligner:
MGA (not open source)
MLAGAN
DIALIGN(not open source)

there a a plenty more tools...

Even if there are not all open source, they are all free to use (when I'm right..).

hope that helps

boetsie · 08-05-2011, 04:45 AM

2) Do not use SSPACE to merge assemblies, SSPACE is for scaffolding or for contig extension. Have a look at this thread for possible assembly mergers;
http://seqanswers.com/forums/showthread.php?t=10834&

3) I think Augustus is a good annotation tool for eurkaryotic genomes: http://augustus.gobics.de/ Haven't used it myself though.

vyahhi · 12-07-2012, 02:37 AM

You can use QUAST (QUality ASsesment Tool for Genome Assembly) to compare multiple genome assemblies:
http://bioinf.spbau.ru/quast
http://sourceforge.net/p/quast
http://http://quast.bioinf.spbau.ru (QUAST server, beta)

neu · 07-23-2014, 04:58 AM

Hi all,
me working with transcriptome data. i have two transcriptomes of superior and inferior traits of a plant. what i did is that i assembled my transcriptomes to a reference genome. now i want to compare the reference assembly to find the difference, ie to find the difference between the inferior and superior one and if possible to find the genes responsible for the quality. i would also like to know about the expression. my lab has CLC bio, and would appreciate any suggestions to my query which make use of CLC bio

Thank You

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08-04-2011, 09:25 PM	#1
megh Junior Member Location: HK Join Date: Jun 2011 Posts: 2	Comparing and merging genome assemblies Hi, We have recently completed the de-novo assembly of a eukaryotic genome. The genome size is ~3.1GB. We used two different assembly platforms/pipelines and got ~2.0GB and ~2.8GB scaffolds respectively. I look for your suggestions in the following areas: 1) What would be the most suitable way to compare the similarity and/or differences between two assemblies? 2) Any suitable assembly merger? The objective of question (1) is to merge them to make it larger. [ I could not install GAM (Genome Assembly Merger) on my MAC OSX 10.6 ] 3) Any suitable and open-source pipeline for annotation? Regards.

08-05-2011, 02:31 AM	#2
colindaven Senior Member Location: Germany Join Date: Oct 2008 Posts: 415	1) Blast is nice, visualised with Circos. Perhaps try circoletto ? 2) Apparently SSPACE is quite good, haven't tried it yet myself.

08-05-2011, 04:21 AM	#3
sphil Senior Member Location: Stuttgart, Germany Join Date: Apr 2010 Posts: 192	Actually there are some genome aligners. They differ in speed, amount of genomes which can be aligned and spped. For a first sigh you can use: Whole genome aligner: MUMer LAGAN AVID (not open source) or Multi Genome aligner: MGA (not open source) MLAGAN DIALIGN(not open source) there a a plenty more tools... Even if there are not all open source, they are all free to use (when I'm right..). hope that helps

08-05-2011, 04:45 AM	#4
boetsie Senior Member Location: NL, Leiden Join Date: Feb 2010 Posts: 245	2) Do not use SSPACE to merge assemblies, SSPACE is for scaffolding or for contig extension. Have a look at this thread for possible assembly mergers; http://seqanswers.com/forums/showthread.php?t=10834& 3) I think Augustus is a good annotation tool for eurkaryotic genomes: http://augustus.gobics.de/ Haven't used it myself though.

12-07-2012, 02:37 AM	#5
vyahhi Junior Member Location: St. Petersburg / San Diego Join Date: Feb 2011 Posts: 4	You can use QUAST (QUality ASsesment Tool for Genome Assembly) to compare multiple genome assemblies: http://bioinf.spbau.ru/quast http://sourceforge.net/p/quast http://http://quast.bioinf.spbau.ru (QUAST server, beta)

07-23-2014, 04:58 AM	#6
neu Junior Member Location: India Join Date: Jul 2014 Posts: 3	Hi all, me working with transcriptome data. i have two transcriptomes of superior and inferior traits of a plant. what i did is that i assembled my transcriptomes to a reference genome. now i want to compare the reference assembly to find the difference, ie to find the difference between the inferior and superior one and if possible to find the genes responsible for the quality. i would also like to know about the expression. my lab has CLC bio, and would appreciate any suggestions to my query which make use of CLC bio Thank You