SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
RNA-Seq: MATS: a Bayesian framework for flexible detection of differential alternativ Newsbot! Literature Watch 0 01-24-2012 03:00 AM
help to install 'FAR - The Flexible Adapter Remover' on Mac OS joseph Bioinformatics 19 01-17-2012 02:46 PM
PubMed: A flexible and efficient template format for circular consensus sequencing an Newsbot! Literature Watch 0 06-24-2010 03:00 AM
BEDTools: A flexible suite of utilities for comparing genomic features nilshomer Literature Watch 5 02-01-2010 10:36 AM
SeqMonk - Flexible analysis of mapped reads simonandrews Bioinformatics 7 07-24-2009 05:12 AM

Reply
 
Thread Tools
Old 08-10-2011, 10:43 PM   #1
bogdan
Member
 
Location: san diego

Join Date: Jul 2008
Posts: 35
Default flexible aligners

Dear all,

please could you let me know the NG-seq aligner that is both fast and very flexible in terms of the insertions/deletions/mismatches ? thanks,

Bogdan
bogdan is offline   Reply With Quote
Old 08-11-2011, 09:20 AM   #2
volks
Member
 
Location: hd.de

Join Date: Jun 2010
Posts: 81
Default

if you are talking about small indels my choice would be BWA.
volks is offline   Reply With Quote
Old 08-11-2011, 07:39 PM   #3
zee
NGS specialist
 
Location: Malaysia

Join Date: Apr 2008
Posts: 249
Default

Novoalign (www.novocraft.com) is also worth looking at. It offers a few more user-friendly options and alignment features than BWA.

There is also BFAST, and stampy.

Quote:
Originally Posted by volks View Post
if you are talking about small indels my choice would be BWA.
zee is offline   Reply With Quote
Old 08-11-2011, 08:14 PM   #4
nilshomer
Nils Homer
 
nilshomer's Avatar
 
Location: Boston, MA, USA

Join Date: Nov 2008
Posts: 1,285
Default

SHRIMP2 too.
nilshomer is offline   Reply With Quote
Old 08-12-2011, 01:10 AM   #5
gaffa
Member
 
Location: Gothenburg/Uppsala, Sweden

Join Date: Oct 2010
Posts: 82
Default

Stampy is good for aligning divergent reads with indels - it is not fast however, but it can be run in hybrid-mode with BWA to speed things up.
gaffa is offline   Reply With Quote
Old 08-17-2011, 03:03 PM   #6
dreesbl
Registered Vendor
 
Location: Seattle, WA

Join Date: Nov 2009
Posts: 6
Default

@bogdan

If you're interested, Spiral Genetics is launching a remote NGS analysis software pipeline that includes a fast-running gapped aligner that is a distributed adaptation of BWA's functionality. We're looking for researchers to test its performance with their data. You could run your reads single and run them double to see the effects on your downstream results. You can contact me via email or with a direct message through the forum if you're interested.

[email protected]
www.spiralgenetics.com
dreesbl 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 12:21 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2018, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO