NGS data

Hello,
I am new to jalview. Can you open and view NGS from jalview?

Kind Regards,
Michy

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Michelle Simon
Bioinformatics,
MRC Mammalian Genetics Unit,
Harwell, Oxon, ox11 0rd, U.K.
E-mail: m.simon@har.mrc.ac.uk
Telephone: +44 (0)1235 841031
www: http://www.har.mrc.ac.uk/

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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:

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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.