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Old 12-02-2016, 08:53 PM   #1
Jayakumar S
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Location: India

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Default Genome alignment

Hi,
Planning to align the scaffolds with the reference genome already available. The size of the reference genome is about 3 gb.
Kindly suggest any suitable methods/softwares for the same.
Presently I am trying with MUMmer 2.

regards,
Jayakumar S
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Old 12-03-2016, 07:36 AM   #2
fahmida
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You may try Quast:
http://bioinf.spbau.ru/en/quast
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Old 12-04-2016, 04:30 PM   #3
Jayakumar S
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Thank you for the suggestion.
Will try for that and let you know.

Jayakumar S
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Old 12-04-2016, 04:45 PM   #4
GenoMax
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If the scaffolds are long (e.g. 10's of kb) then you may want to use LASTZ.
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Old 12-04-2016, 08:30 PM   #5
Ali May
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Default

From my experience what tool to use depends on why you want to do the assembly.

The last time I wanted to order scaffolds I used Mauve, but this was for a 3 MB genome with less than 15 scaffolds.

You might also want to have a look at
https://omictools.com/whole-genome-alignment-category
and
https://www.biostars.org/p/3511/

I personally make good use of the dev version of BRIG when I want to quickly see how my scaffolds map to a reference microbial genome.
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