Detecting SNPs with helioscope

[lbragg]

Hi forum,

Just wondering - can anyone recommend an open source tool for SNP detection which uses helioscope reads against a genome assembly? Helicos say on their site that they will be making an alignment tool available soon - but it does not seem to be available just now.

In addition - can anyone recommend tools for visualising the alignment and SNP call.

Thanks in advance!

[ramouz87]

Hi,
the resequencing pipline that is part of the helisphere suite
allows that it loads the sms files and give you a table with discovred SNP.
if you have already aligned the reads you can directely use snpSniffer
one other alternative is to use varscan on aligned reads aswell it works but you have a reduced list and there's a reduced list of overlapping SNP.

for visualisation,
I would recommend tablet & IGV

Hope this will help

Best,
Ramzi

[Lee Sam]

Isn't IndexDP available on the Heliosphere? You need to use an aligner that allows indels because of the characteristics of the Helicos sequencer (e.g. dark base incorporation).

[lbragg]

Thanks for the advice! I haven't worked with this platform before