SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Question: Reference assisted genome assembly - TOOLS Patrice Bioinformatics 1 09-13-2016 02:33 AM
help needed: reference guided assembly of bacterial genomes? jerrybug109 Bioinformatics 4 02-29-2016 09:42 AM
Compare de-novo transcriptome assembly to genome reference guided assembly IdoBar Bioinformatics 1 04-04-2014 12:28 AM
Reference guided assembly StopCodon De novo discovery 5 06-25-2013 09:49 AM
bacterial consensus sequence reference guided assembly Kerensa Bioinformatics 0 01-10-2011 08:38 PM

Reply
 
Thread Tools
Old 01-14-2017, 03:48 AM   #1
capricy
Senior Member
 
Location: 63130

Join Date: Apr 2012
Posts: 125
Default looking for reference-guided genome assembly tools

Hello, there,

I got the illumina data from two E coli isolate genomic DNA and try to do the assembly. There are many de novo assemblers around. I just wonder if there are any tools for reference-based assembler since this bacterium has reference deposit.

Thank you very much for any input!

C
capricy is offline   Reply With Quote
Old 01-15-2017, 01:30 PM   #2
mastal
Senior Member
 
Location: uk

Join Date: Mar 2009
Posts: 667
Default

Velvet has options for reference-guided assembly. See the velvet webpage. I think the module for assembly using a reference is called Columbus, and there is a manual.

https://www.ebi.ac.uk/~zerbino/velvet


https://www.ebi.ac.uk/~zerbino/velve...bus_manual.pdf


I'm pretty sure you can also do reference-based assembly with Mira.

Last edited by mastal; 01-15-2017 at 01:40 PM.
mastal is offline   Reply With Quote
Old 01-16-2017, 01:18 AM   #3
capricy
Senior Member
 
Location: 63130

Join Date: Apr 2012
Posts: 125
Default

Thank you so much for the information. I will explore those methods.

C.
capricy is offline   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 11:46 AM.


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