[Jalview-discuss] NGS data

[Jim Procter]

Hello Michy

I remember your email from back in January 2009, when you asked about 
tools to convert .ace files to any NGS format.

None of the current versions of Jalview will cope perfectly with NGS 
scale data, although it is possible to read in a whole reference genome 
+ aligned reads, you will need a machine with considerable amounts of 
RAM (6G at the very least) to work with jalview projects containing such 
alignments, and some operations (e.g. sequence selection and group 
creation) will be very slow. I hope to devote a whole development period 
to improving this situation next year, including the introduction of 
support for some of the common NGS formats (such SAM and BAM which can 
be manipulated using SAMtools). If there are specific formats that your 
institute works with, then do let me know and I'll see if I can 
incorporate them.

Until then, I can only suggest you explore some of the existing NGS 
readers. One that I know of is Tablet (http://bioinf.scri.ac.uk/tablet/) 
written by Iain Milne, who also developed the TOPAli application for 
evolutionary analysis (one of the tools that was supported by the VAMSAS 
project).

All the best,
Jim Procter.

michy wrote:
> Hello,
> I am new to jalview.  Can you open and view NGS from jalview?
>
> Kind Regards,
> Michy
>
>   


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J. B. Procter  (JALVIEW/ENFIN)  Barton Bioinformatics Research Group
Phone/Fax:+44(0)1382 388734/345764  http://www.compbio.dundee.ac.uk
The University of Dundee is a Scottish Registered Charity, No. SC015096.