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Old 01-27-2010, 05:05 AM   #1
scientifica
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Default Quick and dirty?

Hi everyone,

I have just received data from the Illumina GAII, but I am still waiting for my software to arrive.
Does anyone happen to know freeware/scripts with which I can easily align and calculate coverage, just for a quick glance at the results?

Thanks!
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Old 01-27-2010, 05:16 AM   #2
strob
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fastx toolkit: http://hannonlab.cshl.edu/fastx_toolkit/
galaxy: http://main.g2.bx.psu.edu/
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Old 01-27-2010, 05:17 AM   #3
jjohnson
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Hey Scientifica, welcome to seqanswers and good luck with your research. I would check out http://seqanswers.com/forums/showthread.php?t=43 which details SW packages for NGS data analysis. Personal favs are Bowtie, MOSAIK, SOAP or ABySS (if you have a grid you have access to).

Then, as you encounter issues or have questions on any of those packages, they are mostlikely already answered and you can run a quick search and read some threads - drop a line in a new thread.

Good Luck.
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Old 01-27-2010, 06:47 AM   #4
krobison
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Also check out the software Wiki
http://seqanswers.com/wiki/Special:BrowseData

BWA is another fast aligner worth looking at. The IGV is a good viewer.

Enjoy!
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Old 01-27-2010, 10:25 PM   #5
Natalya
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MAQ by Li Heng, Sanger
http://maq.sourceforge.net/

SOAP by Li Ruiqiang, BGI
http://soap.genomics.org.cn/
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Old 01-27-2010, 11:53 PM   #6
simonandrews
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Once you've aligned your data (or if you have the Eland files from your Illumina run), then if you're using one of the common eukaryotic species you should be able to view it really quickly in SeqMonk. Just unzip it, run it and load in your data.
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