SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
How to align SNP coordinates against a circular reference genome? Lspoor General 1 02-17-2012 10:44 AM
Assemble tools dicty Bioinformatics 8 02-23-2011 01:02 AM
cufflink assemble result syslm01 Bioinformatics 2 07-16-2010 10:19 PM
cufflinks assemble syslm01 Bioinformatics 0 05-05-2010 03:43 AM
Do we still need to assemble a genome? bp2010 Bioinformatics 6 01-28-2010 06:23 PM

Reply
 
Thread Tools
Old 04-30-2009, 05:51 AM   #1
anyone1985
Member
 
Location: shanghai, chia

Join Date: Mar 2009
Posts: 67
Default Who is the best way to align/assemble to a reference?

There are so many software to mapping the solexa/SOLid reads to reference. Which is the best?
anyone1985 is offline   Reply With Quote
Old 04-30-2009, 06:24 AM   #2
francesco.vezzi
Member
 
Location: Udine (Italy)

Join Date: Jan 2009
Posts: 50
Default

Quote:
Originally Posted by anyone1985 View Post
There are so many software to mapping the solexa/SOLid reads to reference. Which is the best?
If you wont to align against a reference sequence more or less all the software are pretty good. They differ a bit from what concern speed and sensitivity but more or less are similar. In my lab we use our own tool that is more sensitive then ELAND and it has performances similar to BOWTIE an SOAP.

For what concern assembly the best software is VELVET. I use also EULER-SR that is some cases perform better then VELVET.
Also EDANA is pretty good but VELVET and EULER are better...
francesco.vezzi is offline   Reply With Quote
Old 04-30-2009, 12:09 PM   #3
nilshomer
Nils Homer
 
nilshomer's Avatar
 
Location: Boston, MA, USA

Join Date: Nov 2008
Posts: 1,285
Default

Quote:
Originally Posted by anyone1985 View Post
There are so many software to mapping the solexa/SOLid reads to reference. Which is the best?
As a biased alignment tool author, I would suggest BFAST for indels and sensitivity.

https://secure.genome.ucla.edu/index.php/BFAST
nilshomer is offline   Reply With Quote
Old 04-30-2009, 05:40 PM   #4
anyone1985
Member
 
Location: shanghai, chia

Join Date: Mar 2009
Posts: 67
Default

Thanks. When I assembled my data, I found the velvet was pretty good. And, I also tried to extend the sequences by different aligment. I would like to find more software with various ideas to help me finish my genome.

Quote:
Originally Posted by francesco.vezzi View Post
If you wont to align against a reference sequence more or less all the software are pretty good. They differ a bit from what concern speed and sensitivity but more or less are similar. In my lab we use our own tool that is more sensitive then ELAND and it has performances similar to BOWTIE an SOAP.

For what concern assembly the best software is VELVET. I use also EULER-SR that is some cases perform better then VELVET.
Also EDANA is pretty good but VELVET and EULER are better...
anyone1985 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 11:07 AM.


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