I know this has been covered before but I also know that the answer is often "it depends". So here is a brief description of what I am trying to do.
I am new to NGS and working on sequencing small (1 Mb) bacterial genomes (http://seqanswers.com/forums/showthread.php?t=24214). I have sequence data for 3 isolates and it appears that I have many gaps (about 80) in each of the assemblies as a result of repeats. So for finishing I have been doing de novo assembly with Newbler, moving contigs with Mauve, and using Ugene for alignments and primer design. This is a lot of work and will get expensive .
Thus far I have been restricted to using Windows for analysis beyond the Newbler assembly. I have been given the go ahead to purchase a computer to install Linux and give me more options for data analysis. But without the experience I am not sure it will necessarily help me out.
Does it seem worthwhile to go ahead with purchase? Will I be able to improve my assemblies and reduce the amount of bench work needed for finishing? Convince me! What kind of computing requirements am I looking at?
I am new to NGS and working on sequencing small (1 Mb) bacterial genomes (http://seqanswers.com/forums/showthread.php?t=24214). I have sequence data for 3 isolates and it appears that I have many gaps (about 80) in each of the assemblies as a result of repeats. So for finishing I have been doing de novo assembly with Newbler, moving contigs with Mauve, and using Ugene for alignments and primer design. This is a lot of work and will get expensive .
Thus far I have been restricted to using Windows for analysis beyond the Newbler assembly. I have been given the go ahead to purchase a computer to install Linux and give me more options for data analysis. But without the experience I am not sure it will necessarily help me out.
Does it seem worthwhile to go ahead with purchase? Will I be able to improve my assemblies and reduce the amount of bench work needed for finishing? Convince me! What kind of computing requirements am I looking at?
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