SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Iontorrent denovo and reference assembler tools pari_89 Bioinformatics 3 05-14-2013 06:47 AM
tools for assembling large contigs shuang Bioinformatics 2 02-29-2012 11:08 PM
alignment and reference genome assembling slny Bioinformatics 3 03-16-2011 06:49 AM
visualization tools for sequence alignments and assembling dicty Bioinformatics 4 03-01-2011 12:48 PM
454 assembling against reference genome donniemarco 454 Pyrosequencing 2 08-17-2009 06:22 AM

Reply
 
Thread Tools
Old 06-18-2013, 10:20 AM   #1
pari_89
Member
 
Location: Newcastle upon Tyne

Join Date: Apr 2013
Posts: 55
Default Assembling against a reference Tools

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.
pari_89 is offline   Reply With Quote
Old 06-18-2013, 10:33 AM   #2
GenoMax
Senior Member
 
Location: East Coast USA

Join Date: Feb 2008
Posts: 7,049
Default

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

Source available here: http://bioen-compbio.bioen.illinois.edu/RACA/
GenoMax is online now   Reply With Quote
Old 06-18-2013, 11:03 AM   #3
pari_89
Member
 
Location: Newcastle upon Tyne

Join Date: Apr 2013
Posts: 55
Default

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.
pari_89 is offline   Reply With Quote
Old 06-18-2013, 06:33 PM   #4
krobison
Senior Member
 
Location: Boston area

Join Date: Nov 2007
Posts: 747
Default

MIRA will assemble against a reference
krobison is offline   Reply With Quote
Old 06-19-2013, 01:12 AM   #5
pari_89
Member
 
Location: Newcastle upon Tyne

Join Date: Apr 2013
Posts: 55
Default

Quote:
Originally Posted by krobison View Post
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
pari_89 is offline   Reply With Quote
Old 06-19-2013, 02:34 AM   #6
mastal
Senior Member
 
Location: uk

Join Date: Mar 2009
Posts: 667
Default Assembling against a reference Tools

If you are running newbler from the command line, the command for running assemblies is 'runAssembly'.
mastal is offline   Reply With Quote
Old 06-19-2013, 08:26 AM   #7
pari_89
Member
 
Location: Newcastle upon Tyne

Join Date: Apr 2013
Posts: 55
Default

Quote:
Originally Posted by mastal View Post
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
pari_89 is offline   Reply With Quote
Old 05-12-2014, 12:46 AM   #8
sabiha
Junior Member
 
Location: hyderabad

Join Date: Mar 2014
Posts: 4
Default

Hii,,

Did any one run RACA ? if so can you help me out in running it?
sabiha is offline   Reply With Quote
Old 05-12-2014, 04:15 AM   #9
GenoMax
Senior Member
 
Location: East Coast USA

Join Date: Feb 2008
Posts: 7,049
Default

Quote:
Originally Posted by sabiha View Post
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?
GenoMax is online now   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 11:57 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO