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Newbie here - I am writing a paper on Sequencing Companies and have a few questions.. KenFlo1 General 10 06-17-2011 10:24 AM
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Many, many dumb newbie questions GerryB Bioinformatics 3 04-23-2010 02:16 AM

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Old 05-04-2010, 11:34 AM   #1
jkersh
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Location: boulder, co

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Default Newbie questions on computers and programs

Hi, I have just started a project that involves resequencing E. coli strains to identify SNPs and have no idea where to go for information. We have access to an Illumina GA system but have no idea what kind of software we would need to align to a reference genome or call SNPs. Additionally we are interested in using barcodes to save some money by multiplexing. I have a good idea that we will be purchasing a computer to handle everything, but all of the information I have found tells me what I need for handling significantly larger genomes.

If anyone has any experience working with smaller and less complex bacterial genomes I could really use the help, nobody around here does anything except worm and human.
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Old 05-05-2010, 04:16 PM   #2
HESmith
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I'm currently analyzing the same type of data (SNPs and indels from bar-coded E. coli mutants). I'm using BFAST (available at www.sourceforge.net) and SAMtools on a desktop workstation (four Xeon CPUs, 6 GB RAM, 500 GB drive). I'll probably double the amount of RAM so everything will run faster, but otherwise it's fine for my purposes.

Harold

P.S.-This set-up would probably work for worms, too (at least, I hope it will), but is not adequate for humans.
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