Assembling against a reference Tools

[pari_89]

Hi again Everyone,

I need to assemble reads of Ion-Torrent data against a reference? Can you please suggest me tools that I can use to do so and possibly tell me how to evaluate the quality of assembling against a reference.

I have Newbler already installed on the cloud? does newbler assemble against a reference. What is its ouputs and how to compare between different reference assembly tools

I do not need aligners(Bowtie etc...) but reference-assemblers or is there any difference between that?

Thank you

Kind Regards

Parinita.

[GenoMax]

Something like this? http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3562798/

Source available here: http://bioen-compbio.bioen.illinois.edu/RACA/

[pari_89]

Thanks but I am looking for something like CLCworkbench option - map reads against a reference. A set of reads that mapped or did not. But I will try looking in RACA as well. I am working with bacterial genomes.

[krobison]

MIRA will assemble against a reference

[pari_89]

MIRA will assemble against a reference

Hi, I have CLCworkbench,mira and trying out runMapper of newbler. I do not know whether it assembles though.


Thanks again

Cheers

Parinita

[mastal]

Assembling against a reference Tools

If you are running newbler from the command line, the command for running assemblies is 'runAssembly'.

[pari_89]

If you are running newbler from the command line, the command for running assemblies is 'runAssembly'.

Yes, I ran the runAssembly command, but this is for de-novo assembly. I want to assemble reads against a reference.

Thank you

Kind Regards

Parinita

[sabiha]

Hii,,

Did any one run RACA ? if so can you help me out in running it?

[GenoMax]

Hii,,

Did any one run RACA ? if so can you help me out in running it?

You will have to be more specific. Are you getting an error?