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Old 08-04-2011, 09:25 PM   #1
megh
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Location: HK

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Default 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.
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Old 08-05-2011, 02:31 AM   #2
colindaven
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1) Blast is nice, visualised with Circos. Perhaps try circoletto ?

2) Apparently SSPACE is quite good, haven't tried it yet myself.
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Old 08-05-2011, 04:21 AM   #3
sphil
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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
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Old 08-05-2011, 04:45 AM   #4
boetsie
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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.
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Old 12-07-2012, 02:37 AM   #5
vyahhi
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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)
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Old 07-23-2014, 04:58 AM   #6
neu
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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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