Using Geneious to analyse Whole Genome Sequencing data

[Morgane_AUS]

Hi all,

I'm mapping my reads (obtained from the MiSeq) to a reference genome using the Geneious software. It is a small bacterial genome.

Can anyone explain the following stats ?

Identical Sites: 1,801,496 (40.6%) Identical to reference genome ??
Pairwise % Identity: 99.0% Pairwise between what and what ?

Coverage of 4,439,218 bases:
Mean: 222.6 Std Dev: 63.5
Minimum: 0 Maximum: 533
Forward: ? Reverse: ?
Ref-Seq: 99.9% (4,408,919 of 4,411,532)

Does that mean that 99.9% of the reference genome has been covered ?

What does "ungapped length" mean?

The help function in the geneious software is not detailed.. I would appreciate any help !

Thanks !

[GenoMax]

One of the reasons to pay for a commercial software license is to be able to call upon their tech support when needed. Have you contacted them?

What kind of alignment are these results from (an NGS specific method or BLAST)?

[Morgane_AUS]

Yes sorry, I found their support website afterwards..

I installed the Bowtie plugin in Geneious and mapped my fastq files to a reference genome.

[Morgane_AUS]

May I ask what do you use ? Do you do it all on BaseSpace or do you use a command line program ?

I'm a new bee (as you can guess) and I'd like to know about the other available options and what skills are required to run these programs (like R-programming maybe?).

Thanks

[GenoMax]

You can use whatever program you feel comfortable with. If you are familiar with the command line then things would be easy to pick up. If not you can start simple (but if possible learn some basics of Unix: http://korflab.ucdavis.edu/Unix_and_Perl/current.html).

Here is a java aligner that you can use on a PC or Mac. Brian has several examples in this thread to get you started: http://seqanswers.com/forums/showthread.php?t=41057

A recent review of aligners: http://www.hindawi.com/journals/bmri/2014/309650/

[Morgane_AUS]

Thanks heaps for your advice