what is the best software to use to analyze illumina NGS data?

[bbsinfo]

i am using Geneiou pro in our lab to assemble the data from NGS.
How about you guys?

[aleferna]

bwa works fine for me.... but it depends on what are you looking for

[siddharthsameer]

NGS data analysis

bwa works fine for me.... but it depends on what are you looking for

Try geneXplain platform for the NGS analysis

[mcnelson.phd]

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.