Assemble tools

[dicty]

Can anyone suggest a good assemble tool for sequence assembling?

Thanks,

Dicty

[dicty]

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

[JohnN]

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

[aloliveira]

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.

[dicty]

Thanks a lot!

Great information! It's very helpful. Thanks a lot!

[azroger]

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

[aloliveira]

Roger,

The cap3 works very good with Sanger reads also.

[dicty]

Thanks a lot for all the responses. I only have Illumina data right now, but may touch other types of data in the future.

[BaCh]

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.