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Old 02-15-2011, 06:40 AM   #1
dicty
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Default Assemble tools

Can anyone suggest a good assemble tool for sequence assembling?

Thanks,

Dicty
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Old 02-15-2011, 07:08 AM   #2
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Default How to create a GRangesList object for genome not from UCSC?

Hi,

I just downloaded a virus genome and the annotation file from NCBI, but not UCSC. How to create a GRangesList object with the virus genome sequence and annotation file that are not from UCSC?

Thanks,

Dicty
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Old 02-15-2011, 12:17 PM   #3
JohnN
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Quote:
Originally Posted by dicty View Post
Can anyone suggest a good assemble tool for sequence assembling?

Thanks,

Dicty
I prefer mira - which can assemble de novo or to a scaffold. http://www.chevreux.org/projects_mira.html or http://sourceforge.net/apps/mediawik...itle=Main_Page

I believe many SEQanswers people use it, and the author may be on here too.

J
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Old 02-16-2011, 01:27 AM   #4
aloliveira
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Hello,

Try using Velvet (Zerbino and Biney) for me is the softer and exist a good documentation about all the steps in assebly.

Best regards.
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Old 02-16-2011, 06:35 AM   #5
dicty
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Default Thanks a lot!

Great information! It's very helpful. Thanks a lot!
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Old 02-16-2011, 08:26 AM   #6
azroger
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Default ABySS, Newbler, Velvet, SoapDeNovo

Hi -
Regarding sequence assembly, there are a lot of tools available. Many are oriented towards genome assembly from next gen reads. These include ABySS (which is fairly flexible for inputs), Newbler (454 reads), Velvet (good assembler but high memory needs), SoapDeNovo (Illumina reads, fairly efficient). For assembling smaller amounts of data from Sanger sequencing or elsewhere, Phrap or Muscle can be good tools.

Roger
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Old 02-16-2011, 08:28 AM   #7
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Roger,

The cap3 works very good with Sanger reads also.
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Old 02-17-2011, 11:47 AM   #8
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Thanks a lot for all the responses. I only have Illumina data right now, but may touch other types of data in the future.
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Old 02-23-2011, 01:02 AM   #9
BaCh
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Quote:
Originally Posted by JohnN View Post
I believe many SEQanswers people use it, and the author may be on here too.
He is, though more easily reachable via the MIRA talk mailing list ... I unfortunately do not have enough time nowadays to scan SEQanswers everyday

B.
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