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Old 04-14-2011, 12:00 AM   #1
Anelda
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Location: Cape Town, South Africa

Join Date: May 2010
Posts: 30
Default LifeScope Genomic Analysis Solutions

Hi there,

I am trying to find out what the community thinks of the SOLiD software. Does anyone have experience using it? How does it compare with something like Galaxy (except, of course that it's not open source, extendible, etc).

Our local sequencing service provider have purchased a license and we would like to know what other software (open source or commercial) he would need to point his clients to for downstream analysis.

Any comments welcome!

Thanks,
Anelda
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Old 02-23-2012, 01:36 PM   #2
seq_lover
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Location: Memphis

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Default

Lifescope comes with all the tertiary analysis (SNP calling, indel, annotation) modules. They have a very nice mapping analysis. I was able to map ~75-85% of total reads to ref genome at mapping quality of 20. The organism sequenced is sub strain of the reference organism. Few problems I faced and still facing:

1) If you run big dataset then lifescope gives time-out error. Sometimes if you are lucky it will finish the job without any problem. We have installed a powerful cluster with 12 nodes and 192 processors and with each node having 1 TB space and local scratch. But still sometime lifescope fails to run a moderate job.

2) CNV analysis is only for human genome? so you cant use it for rat or mouse.

3) Lifescope produces one bam file for each lane of data. Somewhere in the manual they say that you should not merge those bam files. I dont know what to do if I need to use some third party tool for my analysis that requires one big bam file.

4) No third party tools are required for installation. It comes with all the dependencies but you should have required cluster system.
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