SEQanswers

Go Back   SEQanswers > Sequencing Technologies/Companies > Illumina/Solexa



Similar Threads
Thread Thread Starter Forum Replies Last Post
QDD, a free software to analyze microsatellites from NGS data martinjf Bioinformatics 3 07-31-2019 12:36 AM
Help to analyze Illumina HiSeq 2000 Human data kiradi Bioinformatics 4 12-09-2011 04:30 AM
SeqSolve: the new NGS software solution for RNA-seq data profiling, from Integromics integromics Vendor Forum 0 01-24-2011 07:30 AM
Analyzing NGS-data for dummies/biologists: suggestions for software? MicroOmicsMan Bioinformatics 6 12-22-2009 07:46 PM
Discussion the general pipeline to analyze 454, Illumina/Solexa data edge General 1 09-09-2009 06:29 PM

Reply
 
Thread Tools
Old 01-18-2012, 11:25 AM   #1
bbsinfo
Member
 
Location: Mars

Join Date: Apr 2011
Posts: 19
Default what is the best software to use to analyze illumina NGS data?

i am using Geneiou pro in our lab to assemble the data from NGS.
How about you guys?
bbsinfo is offline   Reply With Quote
Old 01-18-2012, 11:31 AM   #2
aleferna
Senior Member
 
Location: sweden

Join Date: Sep 2009
Posts: 121
Default

bwa works fine for me.... but it depends on what are you looking for
aleferna is offline   Reply With Quote
Old 08-21-2013, 12:03 AM   #3
siddharthsameer
Junior Member
 
Location: germany

Join Date: Aug 2013
Posts: 9
Default NGS data analysis

Quote:
Originally Posted by aleferna View Post
bwa works fine for me.... but it depends on what are you looking for
Try geneXplain platform for the NGS analysis
siddharthsameer is offline   Reply With Quote
Old 08-21-2013, 04:48 AM   #4
mcnelson.phd
Senior Member
 
Location: Connecticut

Join Date: Jul 2011
Posts: 162
Default

We have and use both Geneious and CLC Genomics Workbench, along with a smattering of command line based programs.

Personally, I prefer Geneious for 90% of my work as I find that it's easier to use and the interface is faster than CLC. The read mapping function will show the ends of reads that extend off the reference, which is a useful feature. The display of most features (annotations, etc) is also better in my opinion and new people find it much easier to use than CLC.

However, CLC is much better at handling our assembly workflows because it's designed specifically for doing that kind of stuff. The CLC interface, is much less intuitive than Geneious though, and I find that it's also less responsive, especially if you have large read mapping files open.

I have no issues with any of the command line programs we use, often because they're the only good option for specific things.

I guess a lot of it comes down to how much money you have to dedicate to bioinformatics apps (CLC = $$$$, Geneious = $/$$, command line programs = free usually), and personal preference.
mcnelson.phd 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 10:08 PM.


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